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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE POLY(ADP-RIBOSE) GLYCOHYDROLASE (PARG) CATALYTIC DOMAIN WITH ADPRIBOSE
 
Authors :  Z. Wang, Z. Cheng, W. Xu
Date :  21 Oct 13  (Deposition) - 29 Jan 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Poly(Adp-Ribose) Glycohydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Wang, J. P. Gagne, G. G. Poirier, W. Xu
Crystallographic And Biochemical Analysis Of The Mouse Poly(Adp-Ribose) Glycohydrolase.
Plos One V. 9 86010 2014
PubMed-ID: 24465839  |  Reference-DOI: 10.1371/JOURNAL.PONE.0086010

(-) Compounds

Molecule 1 - POLY(ADP-RIBOSE) GLYCOHYDROLASE
    Chains: A, B, C
    EC Number: 3.2.1.143
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN
    Gene: PARG
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 36)

Asymmetric Unit (3, 36)
No.NameCountTypeFull Name
1AR63Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGENPHOSPHATE
2IOD6Ligand/IonIODIDE ION
3MSE27Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1AR61Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGENPHOSPHATE
2IOD2Ligand/IonIODIDE ION
3MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1AR61Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGENPHOSPHATE
2IOD2Ligand/IonIODIDE ION
3MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (3, 12)
No.NameCountTypeFull Name
1AR61Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGENPHOSPHATE
2IOD2Ligand/IonIODIDE ION
3MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:662 , LYS A:668BINDING SITE FOR RESIDUE IOD A 1001
2AC2SOFTWARETYR A:514BINDING SITE FOR RESIDUE IOD A 1002
3AC3SOFTWARETHR A:718 , ILE A:719 , GLU A:720 , PHE A:731 , ASN A:733 , GLY A:738 , VAL A:746 , GLN A:747 , GLU A:748 , GLU A:749 , TYR A:785 , TYR A:788 , ASN A:862 , GLY A:864 , CYS A:865 , GLY A:866 , ALA A:867 , PHE A:868 , PHE A:895BINDING SITE FOR RESIDUE AR6 A 1003
4AC4SOFTWARELYS B:668BINDING SITE FOR RESIDUE IOD B 1001
5AC5SOFTWARETYR B:514BINDING SITE FOR RESIDUE IOD B 1002
6AC6SOFTWAREILE B:719 , GLU B:720 , PHE B:731 , ASN B:733 , GLY B:738 , VAL B:746 , GLN B:747 , GLU B:748 , GLU B:749 , TYR B:785 , TYR B:788 , ASN B:862 , GLY B:864 , CYS B:865 , GLY B:866 , ALA B:867 , PHE B:868 , PHE B:895BINDING SITE FOR RESIDUE AR6 B 1003
7AC7SOFTWARESER C:662 , LYS C:665 , LYS C:668BINDING SITE FOR RESIDUE IOD C 1001
8AC8SOFTWARETYR C:514BINDING SITE FOR RESIDUE IOD C 1002
9AC9SOFTWAREILE C:719 , GLU C:720 , PHE C:731 , ASN C:733 , GLY C:738 , VAL C:746 , GLN C:747 , GLU C:748 , GLU C:749 , TYR C:788 , ASN C:862 , GLY C:864 , GLY C:866 , ALA C:867 , PHE C:868 , PHE C:895BINDING SITE FOR RESIDUE AR6 C 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NA0)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Mse A:457 -Pro A:458
2Phe A:491 -Pro A:492
3Mse B:457 -Pro B:458
4Phe B:491 -Pro B:492
5Mse C:457 -Pro C:458
6Phe C:491 -Pro C:492

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NA0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NA0)

(-) Exons   (0, 0)

(no "Exon" information available for 4NA0)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:501
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhh..................eee.........................................hhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeehhhhhhhhhhhhh...........hhhhhh....hhhhhh....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh......eeee...hhhhhh...eeeee..............hhhhhhhhhhhhhhhhhhhh......eeeeee.....eeee.hhhhheeeee...............eeeee.......hhhhhhhhhhhhhhhhhhhhhh....hhhhh..eeee.........hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4na0 A 444 KKWLGTPIEEmRKmPRCGIHLPSLRPSASHTVTVRVDLLRAGEVPKPFPTHYKDLWDNKHVKmPCSEQNLYAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALVDFWDKVLEEAEAQHLYQSILPDmVKIALCLPNICTQPIPLLKQKmNHSVTmSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEGNGRGmLQVDFANRFVGGGVTGAGLVQEEIRFLINPELIVSRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWARSHEDGSEKDDWQRRCTEIVAIDALHFRRYLDQFVPEKVRRELNKAYCGFLRPGVPSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELmRDIYSmHTFLTERKLDVGKVYKLLLRYYNEECRNCPGPDIKLYPFIYHAVESS 956
                                   453|  |   463       473       483       493       503  |    513||     533       543       553       563       573       583      |593       603       613    |  623       633       643       653       663       673       683       693       703       713       723  |    733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903   |   913       923       933  ||   945       955 
                                    454-MSE                                             506-MSE 514|                                                              590-MSE               612-MSE |                                                                                                         726-MSE                                                                                                                                                                        901-MSE |                          936|                 
                                       457-MSE                                                   525                                                                                          618-MSE                                                                                                                                                                                                                                                                                          907-MSE                       939                 


Chain B from PDB  Type:PROTEIN  Length:502
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhh..................eee..hhhhh..............................ee..eehhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeehhhhhhhhhhhhh....................hhhhhh....hhhhhhhhhhhhhhhhhhh....eeeeeeee................eeee...hhhhhh...eeeee..............hhhhhhhhhhhhhhhhhhhh......eeeeee.....eeee.hhhhheeeee...............eeeee......hhhhhhhhhhhhhhhhhhhhhhh....hhhhh..eeee.........hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4na0 B 444 KKWLGTPIEEmRKmPRCGIHLPSLRPSASHTVTVRVDLLRAGEVPKPFPTHYKDLWDNKHVKmPCSEQNLYTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALVDFWDKVLEEAEAQHLYQSILPDmVKIALCLPNICTQPIPLLKQKmNHSVTmSQEQIASLLANAFFCTFPRRNAKMSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEGNGRGmLQVDFANRFVGGGVTGAGLVQEEIRFLINPELIVSRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWARSHEDGSEKDDWQRRCTEIVAIDALHFRRYLDQFVPEKVRRELNKAYCGFLRPGVPSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELmRDIYSmHTFLTERKLDVGKVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVES 955
                                   453|  |   463       473       483       493       503  |    513||     532       542       552       562       572       582       592       602       612     | 622       632       642|      653       663       673       683       693       703       713       723  |    733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903   |   913       923       933       943       953  
                                    454-MSE                                             506-MSE 514|                                                               590-MSE               612-MSE |                     642|                                                                               726-MSE                                                                                                                                                                        901-MSE |                                                
                                       457-MSE                                                   524                                                                                           618-MSE                  644                                                                                                                                                                                                                                                                    907-MSE                                            


Chain C from PDB  Type:PROTEIN  Length:501
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhh..................eee..hhhhh...................................hhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeehhhhhhhhhhhhh...................hhhhh.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh......eeee.............eeee..............hhhhhhhhhhhhhhhhhhh.......eeeeee.....eeee......eeeee...............eeeee......hhhhhhhhhhhhhhhhhhhhhhh....hhhhh..eeee.........hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4na0 C 444 KKWLGTPIEEmRKmPRCGIHLPSLRPSASHTVTVRVDLLRAGEVPKPFPTHYKDLWDNKHVKmPCSEQNLYTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALVDFWDKVLEEAEAQHLYQSILPDmVKIALCLPNICTQPIPLLKQKmNHSVTmSQEQIASLLANAFFCTFPRRNAKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEGNGRGmLQVDFANRFVGGGVTGAGLVQEEIRFLINPELIVSRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWARSHEDGSEKDDWQRRCTEIVAIDALHFRRYLDQFVPEKVRRELNKAYCGFLRPGVPSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELmRDIYSmHTFLTERKLDVGKVYKLLLRYYNEECRNCSTGPDIKLYPFIYHAVESS 956
                                   453|  |   463       473       483       493       503  |    513||     532       542       552       562       572       582       592       602       612     | 622       632       644       654       664       674       684       694       704       714       724 |     734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894      |904  |    914       924       934   ||  945       955 
                                    454-MSE                                             506-MSE 514|                                                               590-MSE               612-MSE |                    641|                                                                               726-MSE                                                                                                                                                                        901-MSE |                            938|                
                                       457-MSE                                                   524                                                                                           618-MSE                 644                                                                                                                                                                                                                                                                    907-MSE                         940
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4NA0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NA0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NA0)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PARG_MOUSE | O88622: 4fc2 4n9y 4n9z 4na4 4na5 4na6

(-) Related Entries Specified in the PDB File

4fc2 WILD TYPE
4n9y E748Q
4n9z E749Q
4na4
4na5