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Conserved domains on  [gi|254574871|pdb|3GQE|A]
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Chain A, Non-structural protein 3

Protein Classification

macro domain-containing protein( domain architecture ID 15348153)

macro domain-containing protein may bind compounds such as O-acetyl-ADP-ribose, mono- and poly-ADP-ribose, and catalyze reactions such as O-acetyl-ADP-ribose deacetylation and reversal of ADP-ribosylation of mono-ADP-ribosylated substrates; similar to viral non-structural protein 3

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Macro_X_Nsp3-like cd21557
X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The ...
 18-145 2.56e-48

X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The X-domain, also called Mac1, is the macrodomain found in riboviral non-structural protein 3 (Nsp3), including the Nsp3 of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) as well as SARS-CoV-2, and other coronaviruses (alpha-, beta-, gamma-, and deltacoronavirus), among others. The SARS-CoV-2 Nsp3 Mac1 is highly conserved among all CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. It appears to counter host-mediated antiviral ADP-ribosylation, a post-translational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Assays show that the de-MARylating activity leads to a rapid loss of substrate, and that Mac1 could not hydrolyze poly-ADP-ribose; thus, Mac1 is a MAR-hydrolase (mono-ADP ribosylhydrolase). Mac1 was originally named ADP-ribose-1"-phosphatase (ADRP) based on data demonstrating that it could remove the phosphate group from ADP-ribose-1"-phosphate; however, activity was modest and was unclear why this would impact a virus infection. This family also includes the X-domain of Avian infectious bronchitis virus (IBV) strain Beaudette coronavirus that does not bind ADP-ribose; the triple glycine sequence found in the X-domains of SARS-CoV and human coronavirus 229E (HCoV229E), which are involved in ADP-ribose binding, is not conserved in the IBV X-domain. SARS-CoVs have two other macrodomains referred to as the SUD-N (N-terminal subdomain, or Mac2) and SUD-M (middle SUD subdomain, or Mac3) of the SARS-unique domain (SUD), which also do not bind ADP-ribose; these bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). SARS-CoV SUD-N and SUD-M are not included in this group.


:

Pssm-ID: 438957  Cd Length: 127  Bit Score: 152.71  E-value: 2.56e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A       18 EGVIINAANSKGQPGGGVCGALYKKFPESFDL--------QPIEVGKARLVKG--AAKHIIHAVGPNFNKVSeveGDKQL 87
Cdd:cd21557   1 EDVVVNAANENLKHGGGVAGAIYKATGGAFQKesdyikknGPLKVGTAVLLPGhgLAKNIIHVVGPRKRKGQ---DDQLL 77

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
3GQE_A       88 AEAYESIAKIvndnnYKSVAIPLLSTGIFSgnkDRLTQSLNHLLTALDTTDADVAIYC 145
Cdd:cd21557  78 AAAYKAVNKE-----YGSVLTPLLSAGIFG---VPPEQSLNALLDAVDTTDADVTVYC 127
 
Name Accession Description Interval E-value
Macro_X_Nsp3-like cd21557
X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The ...
 18-145 2.56e-48

X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The X-domain, also called Mac1, is the macrodomain found in riboviral non-structural protein 3 (Nsp3), including the Nsp3 of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) as well as SARS-CoV-2, and other coronaviruses (alpha-, beta-, gamma-, and deltacoronavirus), among others. The SARS-CoV-2 Nsp3 Mac1 is highly conserved among all CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. It appears to counter host-mediated antiviral ADP-ribosylation, a post-translational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Assays show that the de-MARylating activity leads to a rapid loss of substrate, and that Mac1 could not hydrolyze poly-ADP-ribose; thus, Mac1 is a MAR-hydrolase (mono-ADP ribosylhydrolase). Mac1 was originally named ADP-ribose-1"-phosphatase (ADRP) based on data demonstrating that it could remove the phosphate group from ADP-ribose-1"-phosphate; however, activity was modest and was unclear why this would impact a virus infection. This family also includes the X-domain of Avian infectious bronchitis virus (IBV) strain Beaudette coronavirus that does not bind ADP-ribose; the triple glycine sequence found in the X-domains of SARS-CoV and human coronavirus 229E (HCoV229E), which are involved in ADP-ribose binding, is not conserved in the IBV X-domain. SARS-CoVs have two other macrodomains referred to as the SUD-N (N-terminal subdomain, or Mac2) and SUD-M (middle SUD subdomain, or Mac3) of the SARS-unique domain (SUD), which also do not bind ADP-ribose; these bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). SARS-CoV SUD-N and SUD-M are not included in this group.


Pssm-ID: 438957  Cd Length: 127  Bit Score: 152.71  E-value: 2.56e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A       18 EGVIINAANSKGQPGGGVCGALYKKFPESFDL--------QPIEVGKARLVKG--AAKHIIHAVGPNFNKVSeveGDKQL 87
Cdd:cd21557   1 EDVVVNAANENLKHGGGVAGAIYKATGGAFQKesdyikknGPLKVGTAVLLPGhgLAKNIIHVVGPRKRKGQ---DDQLL 77

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
3GQE_A       88 AEAYESIAKIvndnnYKSVAIPLLSTGIFSgnkDRLTQSLNHLLTALDTTDADVAIYC 145
Cdd:cd21557  78 AAAYKAVNKE-----YGSVLTPLLSAGIFG---VPPEQSLNALLDAVDTTDADVTVYC 127
A1pp smart00506
Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by ...
 6-127 7.26e-38

Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson _ Fuji).


Pssm-ID: 214701  Cd Length: 133  Bit Score: 126.27  E-value: 7.26e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A           6 YHVVRGDIATATEGVIINAANSKGQPGGGVCGALYKKFP-----ESFDLQP---IEVGKARLVKGA---AKHIIHAVGPN 74
Cdd:smart00506   2 LKVVKGDITKPRADAIVNAANSDGAHGGGVAGAIARAAGkalskEEVRKLAggeCPVGTAVVTEGGnlpAKYVIHAVGPR 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
3GQE_A          75 FNKVSEvEGDKQLAEAYESIAKIVNDNNYKSVAIPLLSTGIFSGNKDRLTQSL 127
Cdd:smart00506  82 ASGHSK-EGFELLENAYRNCLELAIELGITSVALPLIGTGIYGVPKDRSAQAL 133
YmdB COG2110
O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ...
 7-160 7.65e-30

O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441713  Cd Length: 168  Bit Score: 106.80  E-value: 7.65e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A        7 HVVRGDIATATEGVIINAANSKGQPGGGVCGALYKKF-PESFD-------LQPIEVGKARLVKG---AAKHIIHAVGPNF 75
Cdd:COG2110   2 EIVQGDITELDVDAIVNAANSSLLGGGGVAGAIHRAAgPELLEecrrlckQGGCPTGEAVITPAgnlPAKYVIHTVGPVW 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A       76 NKVSEVEgDKQLAEAYESIAKIVNDNNYKSVAIPLLSTGIFSGNKDRLTQ-SLNHLLTALDTTDA--DVAIYCRDKKWEM 152
Cdd:COG2110  82 RGGGPSE-EELLASCYRNSLELAEELGIRSIAFPAIGTGVGGFPWEEAAPiAVETLRDFLEEHPSleEVRFVLFDEEDYE 160


                ....*...
3GQE_A      153 TLKEAVAR 160
Cdd:COG2110 161 AYRRALAR 168
Macro pfam01661
Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ...
 22-116 1.77e-25

Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent: in certain cases it is believed to bind non-covalently; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site.


Pssm-ID: 460286  Cd Length: 116  Bit Score: 94.17  E-value: 1.77e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A         22 INAANSKGQPGGGVCGALYKKFPESF-------DLQPIEVGKARLVKG---AAKHIIHAVGPNFNKVSEVEGDKQLAEAY 91
Cdd:pfam01661   1 VNAANSRLLGGGGVAGAIHRAAGPELleecrelKKGGCPTGEAVVTPGgnlPAKYVIHTVGPTWRHGGSHGEEELLESCY 80

                          90       100
                  ....*....|....*....|....*
3GQE_A         92 ESIAKIVNDNNYKSVAIPLLSTGIF 116
Cdd:pfam01661  81 RNALALAEELGIKSIAFPAISTGIY 105
PRK00431 PRK00431
ADP-ribose-binding protein;
7-116 1.68e-20

ADP-ribose-binding protein;


Pssm-ID: 234759  Cd Length: 177  Bit Score: 82.97  E-value: 1.68e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A         7 HVVRGDIATATEGVIINAANSKGQPGGGVCGALYKK-----------FPESFDlqPIEVGKARLVKG---AAKHIIHAVG 72
Cdd:PRK00431   6 EVVQGDITELEVDAIVNAANSSLLGGGGVDGAIHRAagpeileecreLRQQQG--PCPTGEAVITSAgrlPAKYVIHTVG 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
3GQE_A        73 PNFnKVSEVEGDKQLAEAYESIAKIVNDNNYKSVAIPLLSTGIF 116
Cdd:PRK00431  84 PVW-RGGEDNEAELLASAYRNSLRLAAELGLRSIAFPAISTGVY 126
 
Name Accession Description Interval E-value
Macro_X_Nsp3-like cd21557
X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The ...
 18-145 2.56e-48

X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The X-domain, also called Mac1, is the macrodomain found in riboviral non-structural protein 3 (Nsp3), including the Nsp3 of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) as well as SARS-CoV-2, and other coronaviruses (alpha-, beta-, gamma-, and deltacoronavirus), among others. The SARS-CoV-2 Nsp3 Mac1 is highly conserved among all CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. It appears to counter host-mediated antiviral ADP-ribosylation, a post-translational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Assays show that the de-MARylating activity leads to a rapid loss of substrate, and that Mac1 could not hydrolyze poly-ADP-ribose; thus, Mac1 is a MAR-hydrolase (mono-ADP ribosylhydrolase). Mac1 was originally named ADP-ribose-1"-phosphatase (ADRP) based on data demonstrating that it could remove the phosphate group from ADP-ribose-1"-phosphate; however, activity was modest and was unclear why this would impact a virus infection. This family also includes the X-domain of Avian infectious bronchitis virus (IBV) strain Beaudette coronavirus that does not bind ADP-ribose; the triple glycine sequence found in the X-domains of SARS-CoV and human coronavirus 229E (HCoV229E), which are involved in ADP-ribose binding, is not conserved in the IBV X-domain. SARS-CoVs have two other macrodomains referred to as the SUD-N (N-terminal subdomain, or Mac2) and SUD-M (middle SUD subdomain, or Mac3) of the SARS-unique domain (SUD), which also do not bind ADP-ribose; these bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). SARS-CoV SUD-N and SUD-M are not included in this group.


Pssm-ID: 438957  Cd Length: 127  Bit Score: 152.71  E-value: 2.56e-48
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A       18 EGVIINAANSKGQPGGGVCGALYKKFPESFDL--------QPIEVGKARLVKG--AAKHIIHAVGPNFNKVSeveGDKQL 87
Cdd:cd21557   1 EDVVVNAANENLKHGGGVAGAIYKATGGAFQKesdyikknGPLKVGTAVLLPGhgLAKNIIHVVGPRKRKGQ---DDQLL 77

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
3GQE_A       88 AEAYESIAKIvndnnYKSVAIPLLSTGIFSgnkDRLTQSLNHLLTALDTTDADVAIYC 145
Cdd:cd21557  78 AAAYKAVNKE-----YGSVLTPLLSAGIFG---VPPEQSLNALLDAVDTTDADVTVYC 127
A1pp smart00506
Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by ...
 6-127 7.26e-38

Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson _ Fuji).


Pssm-ID: 214701  Cd Length: 133  Bit Score: 126.27  E-value: 7.26e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A           6 YHVVRGDIATATEGVIINAANSKGQPGGGVCGALYKKFP-----ESFDLQP---IEVGKARLVKGA---AKHIIHAVGPN 74
Cdd:smart00506   2 LKVVKGDITKPRADAIVNAANSDGAHGGGVAGAIARAAGkalskEEVRKLAggeCPVGTAVVTEGGnlpAKYVIHAVGPR 81

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
3GQE_A          75 FNKVSEvEGDKQLAEAYESIAKIVNDNNYKSVAIPLLSTGIFSGNKDRLTQSL 127
Cdd:smart00506  82 ASGHSK-EGFELLENAYRNCLELAIELGITSVALPLIGTGIYGVPKDRSAQAL 133
YmdB COG2110
O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ...
 7-160 7.65e-30

O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441713  Cd Length: 168  Bit Score: 106.80  E-value: 7.65e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A        7 HVVRGDIATATEGVIINAANSKGQPGGGVCGALYKKF-PESFD-------LQPIEVGKARLVKG---AAKHIIHAVGPNF 75
Cdd:COG2110   2 EIVQGDITELDVDAIVNAANSSLLGGGGVAGAIHRAAgPELLEecrrlckQGGCPTGEAVITPAgnlPAKYVIHTVGPVW 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A       76 NKVSEVEgDKQLAEAYESIAKIVNDNNYKSVAIPLLSTGIFSGNKDRLTQ-SLNHLLTALDTTDA--DVAIYCRDKKWEM 152
Cdd:COG2110  82 RGGGPSE-EELLASCYRNSLELAEELGIRSIAFPAIGTGVGGFPWEEAAPiAVETLRDFLEEHPSleEVRFVLFDEEDYE 160


                ....*...
3GQE_A      153 TLKEAVAR 160
Cdd:COG2110 161 AYRRALAR 168
Macro pfam01661
Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ...
 22-116 1.77e-25

Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent: in certain cases it is believed to bind non-covalently; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site.


Pssm-ID: 460286  Cd Length: 116  Bit Score: 94.17  E-value: 1.77e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A         22 INAANSKGQPGGGVCGALYKKFPESF-------DLQPIEVGKARLVKG---AAKHIIHAVGPNFNKVSEVEGDKQLAEAY 91
Cdd:pfam01661   1 VNAANSRLLGGGGVAGAIHRAAGPELleecrelKKGGCPTGEAVVTPGgnlPAKYVIHTVGPTWRHGGSHGEEELLESCY 80

                          90       100
                  ....*....|....*....|....*
3GQE_A         92 ESIAKIVNDNNYKSVAIPLLSTGIF 116
Cdd:pfam01661  81 RNALALAEELGIKSIAFPAISTGIY 105
Macro_Af1521_BAL-like cd02907
macrodomain, Af1521-like family; Macrodomains are found in a variety of proteins with diverse ...
 8-122 2.15e-24

macrodomain, Af1521-like family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. The macrodomains in this family show similarity to Af1521, a protein from Archaeoglobus fulgidus containing a stand-alone macrodomain. Af1521 binds ADP-ribose and exhibits phosphatase activity toward ADP-ribose-1"-monophosphate (Appr-1"-p). Also included in this family are the N-terminal (or first) macrodomains of BAL (B-aggressive lymphoma) proteins which contain multiple macrodomains, such as the first macrodomain of mono-ADP-ribosyltransferase PARP14 (PARP-14, also known as ADP-ribosyltransferase diphtheria toxin-like 8, ATRD8, B aggressive lymphoma protein 2, or BAL2). Most BAL proteins also contain a C-terminal PARP active site and are also named as PARPs. Human BAL1 (or PARP-9) was originally identified as a risk-related gene in diffuse large B-cell lymphoma that promotes malignant B-cell migration. Some BAL family proteins exhibit PARP activity. Poly (ADP-ribosyl)ation is an immediate DNA-damage-dependent post-translational modification of histones and other nuclear proteins. BAL proteins may also function as transcriptional repressors.


Pssm-ID: 394877 [Multi-domain]  Cd Length: 158  Bit Score: 92.55  E-value: 2.15e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A        8 VVRGDIATATEGVIINAANSKGQPGGGVCGALYKKFPESF---------DLQPIEVGKARLVKGA---AKHIIHAVGPNF 75
Cdd:cd02907   6 VYKGDITKEKVDAIVNAANERLKHGGGVAGAISKAGGPEIqeecdkyikKNGKLRVGEVVVTSAGklpCKYVIHAVGPRW 85

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*..
3GQE_A       76 NKVSEVEGDKQLAEAYESIAKIVNDNNYKSVAIPLLSTGIFSGNKDR 122
Cdd:cd02907  86 SGGSKEECEDLLYKAVLNSLEEAEELKATSIAIPAISSGIFGFPLDL 132
Macro_OAADPr_deacetylase cd02908
macrodomain, O-acetyl-ADP-ribose (OAADPr) family; Macrodomains are found in a variety of ...
 7-116 1.66e-22

macrodomain, O-acetyl-ADP-ribose (OAADPr) family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. This family includes eukaryotic macrodomain proteins such as human MacroD1 and MacroD2, and bacterial proteins such as Escherichia coli YmdB; these have been shown to be O-acetyl-ADP-ribose (OAADPr) deacetylases that efficiently catalyze the hydrolysis of OAADPr to produce ADP-ribose and free acetate. OAADPr is a sirtuin reaction product generated from the NAD+-dependent protein deacetylation reactions and has been implicated as a signaling molecule. By acting on mono-ADP-ribosylated substrates, OAADPr deacetylases may reverse cellular ADP-ribosylation.


Pssm-ID: 438955  Cd Length: 166  Bit Score: 87.95  E-value: 1.66e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A        7 HVVRGDIATATEGVIINAANSKGQPGGGVCGALY-----------KKFPesfdlQPIEVGKARLVKG---AAKHIIHAVG 72
Cdd:cd02908   3 SLWRGDITKLEVDAIVNAANSSLLGGGGVDGAIHraagpelleecRKLG-----GVCPTGEAKITPGynlPAKYVIHTVG 77

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
3GQE_A       73 PNFNKVSEVEGDkQLAEAYESIAKIVNDNNYKSVAIPLLSTGIF 116
Cdd:cd02908  78 PIGEGGVEEEPE-LLASCYRSSLELALENGLKSIAFPCISTGIY 120
PRK00431 PRK00431
ADP-ribose-binding protein;
7-116 1.68e-20

ADP-ribose-binding protein;


Pssm-ID: 234759  Cd Length: 177  Bit Score: 82.97  E-value: 1.68e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A         7 HVVRGDIATATEGVIINAANSKGQPGGGVCGALYKK-----------FPESFDlqPIEVGKARLVKG---AAKHIIHAVG 72
Cdd:PRK00431   6 EVVQGDITELEVDAIVNAANSSLLGGGGVDGAIHRAagpeileecreLRQQQG--PCPTGEAVITSAgrlPAKYVIHTVG 83

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
3GQE_A        73 PNFnKVSEVEGDKQLAEAYESIAKIVNDNNYKSVAIPLLSTGIF 116
Cdd:PRK00431  84 PVW-RGGEDNEAELLASAYRNSLRLAAELGLRSIAFPAISTGVY 126
Macro_SF cd02749
macrodomain superfamily; Macrodomains are found in a variety of proteins with diverse cellular ...
 20-127 3.10e-14

macrodomain superfamily; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Macrodomains include the yeast macrodomain Poa1 which is a phosphatase of ADP-ribose-1"-phosphate, a by-product of tRNA splicing. Some macrodomains have ADPr-unrelated binding partners such as the coronavirus SUD-N (N-terminal subdomain) and SUD-M (middle subdomain) of the SARS-unique domain (SUD) which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). Macrodomains regulate a wide variety of cellular and organismal processes, including DNA damage repair, signal transduction, and immune response.


Pssm-ID: 394871  Cd Length: 121  Bit Score: 65.11  E-value: 3.10e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A       20 VIINAANSKGQPGGGVCGALYKKF--------PESFDLQPIEVGKARLVKG---AAKHIIHAVGPNfnKVSEVEGDKQLA 88
Cdd:cd02749   2 AIVNPANNDLYLGGGVAKAISKKAggdlqeecEERKKNGYLKVGEVAVTKGgnlPARYIIHVVGPV--ASSKKKTYEPLK 79

                        90       100       110
                ....*....|....*....|....*....|....*....
3GQE_A       89 EAYESIAKIVNDNNYKSVAIPLLSTGIFSGNKDRLTQSL 127
Cdd:cd02749  80 KCVKNCLSLADEKGLKSVAFPAIGTGIAGFPPEEAARIM 118
Macro_Ttha0132-like cd03330
Macrodomain, uncharacterized family similar to Thermus thermophilus hypothetical protein ...
 8-115 2.10e-11

Macrodomain, uncharacterized family similar to Thermus thermophilus hypothetical protein Ttha0132; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Macrodomains include the yeast macrodomain Poa1 which is a phosphatase of ADP-ribose-1"-phosphate, a by-product of tRNA splicing. Some macrodomains have ADPr-unrelated binding partners such as the coronavirus SUD-N (N-terminal subdomain) and SUD-M (middle subdomain) of the SARS-unique domain (SUD) which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). Macrodomains regulate a wide variety of cellular and organismal processes, including DNA damage repair, signal transduction, and immune response. This family is composed of uncharacterized proteins containing a stand-alone macrodomain, similar to Thermus thermophilus hypothetical protein Ttha0132.


Pssm-ID: 394879  Cd Length: 147  Bit Score: 58.60  E-value: 2.10e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A        8 VVRGDIATATEGVIINAANSKGQPGGGVCGALYKK-----FPESFDLQPIEVGKArLVKGA----AKHIIHAVGPNFNKV 78
Cdd:cd03330   4 VVQGDITEQDADAIVNAANRRLLMGSGVAGAIKRKggeeiEREAMRKGPIRVGEA-VETGAgklpAKYVIHAAVMGMPGR 82

                        90       100       110
                ....*....|....*....|....*....|....*..
3GQE_A       79 SEVEgdkQLAEAYESIAKIVNDNNYKSVAIPLLSTGI 115
Cdd:cd03330  83 SSEE---SIRDATRNALAKAEELGLESVAFPAIGTGV 116
PRK04143 PRK04143
protein-ADP-ribose hydrolase;
10-116 1.05e-10

protein-ADP-ribose hydrolase;


Pssm-ID: 235225  Cd Length: 264  Bit Score: 58.45  E-value: 1.05e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A        10 RGDIATATEGVIINAANSK--G--QPG-----------GGV-----CGALYKK--FPEsfdlqpiEVGKARLVKG---AA 64
Cdd:PRK04143  89 QGDITRLKVDAIVNAANSRllGcfQPNhdcidnaihtfAGVqlrldCAEIMTEqgRKE-------ATGQAKITRAynlPA 161

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
3GQE_A        65 KHIIHAVGPNFNK--VSEVEGDkQLAEAYESIAKIVNDNNYKSVAIPLLSTGIF 116
Cdd:PRK04143 162 KYVIHTVGPIIRKqpVSPIRAD-LLASCYRSCLKLAEKAGLKSIAFCCISTGVF 214
Macro_H2A-like cd02904
macrodomain, macroH2A-like family; Macrodomains are found in a variety of proteins with ...
 8-114 1.15e-08

macrodomain, macroH2A-like family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Members of this family are similar to macroH2A, a variant of the major-type core histone H2A, which contains an N-terminal H2A domain and a C-terminal nonhistone macrodomain. Histone macroH2A is enriched on the inactive X chromosome of mammalian female cells. It does not bind poly ADP-ribose, but does bind the monomeric SirT1 metabolite O-acetyl-ADP-ribose (OAADPR) with high affinity through its macrodomain. This family also includes the ADP-ribose binding macrodomain of the macroH2A variant, macroH2A1.1. The macroH2A1.1 isoform inhibits PARP1-dependent DNA-damage induced chromatin dynamics. The putative ADP-ribose binding pocket of the human macroH2A2 macrodomain exhibits marked structural differences compared with the macroH2A1.1 variant.


Pssm-ID: 394875  Cd Length: 188  Bit Score: 51.93  E-value: 1.15e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A        8 VVRGDIATATEGVIINAANSKGQPGGGVCGALYKKFPESFDLQ---------PIEVGKARLVKG---AAKHIIHAVGPNF 75
Cdd:cd02904  22 VVQGDIASIKADAIVHPTNATFYLGGEVGSALEKAGGKEFVEEvkelrksngPLEVAGAAISPGhnlPAKFVIHCNSPSW 101

                        90       100       110
                ....*....|....*....|....*....|....*....
3GQE_A       76 NKVSEVEgdkQLAEAYESIAKIVNDNNYKSVAIPLLSTG 114
Cdd:cd02904 102 GSDKCEE---LLEKTVKNCLALADEKKLKSVAFPSIGSG 137
Macro_BAL-like cd02903
macrodomain, B-aggressive lymphoma (BAL)-like family; Macrodomains are found in a variety of ...
 8-114 1.31e-08

macrodomain, B-aggressive lymphoma (BAL)-like family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Members of this family show similarity to BAL (B-aggressive lymphoma) proteins, which contain one to three macrodomains. Most BAL family macrodomains belong to this family except for the most N-terminal domain in multiple-domain containing proteins. This family includes the second and third macrodomains of mono-ADP-ribosyltransferase PARP14 (PARP-14, also known as ADP-ribosyltransferase diphtheria toxin-like 8, ATRD8, B aggressive lymphoma protein 2, or BAL2). Most BAL proteins also contain a C-terminal PARP active site and are also named as PARPs. Human BAL1 (or PARP-9) was originally identified as a risk-related gene in diffuse large B-cell lymphoma that promotes malignant B-cell migration. Some BAL family proteins exhibit PARP activity. Poly (ADP-ribosyl)ation is an immediate DNA-damage-dependent post-translational modification of histones and other nuclear proteins. BAL proteins may also function as transcriptional repressors.


Pssm-ID: 394874  Cd Length: 175  Bit Score: 51.49  E-value: 1.31e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3GQE_A        8 VVRGDIATATEGVIINAANSKGQPGGGVCGALYKKFPESFDLQPIEVGKARLVKGAA---------KHIIHAVGPNFNKV 78
Cdd:cd02903  12 LVKGDITKEKTDVIVNSVSSDLLLKGGVSKAILKAAGPELQDECANQGKQPASGDVIvtsggnlpcKYVYHVVLPHYNPG 91

                        90       100       110
                ....*....|....*....|....*....|....*.
3GQE_A       79 SEvegdKQLAEAYESIAKIVNDNNYKSVAIPLLSTG 114
Cdd:cd02903  92 NE----KTLKDIVRKCLEKAENYKMSSISFPAIGTG 123
Macro_GDAP2-like cd02905
macrodomain, GDAP2-like family; Macrodomains are found in a variety of proteins with diverse ...
 55-113 4.35e-04

macrodomain, GDAP2-like family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. This family contains proteins similar to human GDAP2, the ganglioside induced differentiation associated protein 2, whose gene is expressed at a higher level in differentiated Neuro2a cells compared with non-differentiated cells. GDAP2 contains an N-terminal macrodomain and a C-terminal Sec14p-like lipid binding domain. It is specifically expressed in brain and testis.


Pssm-ID: 394876  Cd Length: 169  Bit Score: 38.76  E-value: 4.35e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
3GQE_A       55 GKARLVKG---AAKHIIHAVGPNFNKVSEVEGDKQLAEAYESIAKIVNDNNYKSVAIPLLST 113
Cdd:cd02905  57 GEAKLTKGynlPARYVIHTVGPRYNEKYRTAAESALYSCYRNVLQLAKEHKLRSVAFPVIHS 118
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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