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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE POLY(ADP-RIBOSE) GLYCOHYDROLASE (PARG) CATALYTIC DOMAIN WITH ADP-HPD
 
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 :  2.50
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, Parg, 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, 35)

Asymmetric Unit (3, 35)
No.NameCountTypeFull Name
1A1R3Ligand/Ion5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE
2IOD5Ligand/IonIODIDE ION
3MSE27Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1A1R1Ligand/Ion5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE
2IOD2Ligand/IonIODIDE ION
3MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (3, 11)
No.NameCountTypeFull Name
1A1R1Ligand/Ion5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE
2IOD1Ligand/IonIODIDE ION
3MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (3, 12)
No.NameCountTypeFull Name
1A1R1Ligand/Ion5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE
2IOD2Ligand/IonIODIDE ION
3MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR 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:895 , HOH A:1102 , HOH A:1110BINDING SITE FOR RESIDUE A1R A 1001
2AC2SOFTWARETYR A:514BINDING SITE FOR RESIDUE IOD A 1002
3AC3SOFTWARESER A:662 , LYS A:668BINDING SITE FOR RESIDUE IOD A 1003
4AC4SOFTWAREILE 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:788 , ASN B:862 , GLY B:864 , GLY B:866 , ALA B:867 , PHE B:868 , PHE B:895BINDING SITE FOR RESIDUE A1R B 1001
5AC5SOFTWAREARG B:664BINDING SITE FOR RESIDUE IOD B 1002
6AC6SOFTWAREILE 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 , CYS C:865 , GLY C:866 , ALA C:867 , PHE C:868 , PHE C:895 , HOH C:1105 , HOH C:1113BINDING SITE FOR RESIDUE A1R C 1001
7AC7SOFTWARELYS C:668BINDING SITE FOR RESIDUE IOD C 1002
8AC8SOFTWARETYR C:514BINDING SITE FOR RESIDUE IOD C 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NA4)

(-) Cis Peptide Bonds  (5, 5)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NA4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NA4)

(-) Exons   (0, 0)

(no "Exon" information available for 4NA4)

(-) 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:505
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhh..................eee.....................................ee....eehhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeehhhhhhhhhhhhh.....................hhhhh.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh......eeee...hhhhhh...eeeee..............hhhhhhhhhhhhhhhhhhh.......eeeeee.....eeee.hhhhheeeee...............eeeee......hhhhhhhhhhhhhhhhhhhhhhh....hhhhh..eeee.........hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4na4 A 444 KKWLGTPIEEmRKmPRCGIHLPSLRPSASHTVTVRVDLLRAGEVPKPFPTHYKDLWDNKHVKmPCSEQNLYPVTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALVDFWDKVLEEAEAQHLYQSILPDmVKIALCLPNICTQPIPLLKQKmNHSVTmSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEGNGRGmLQVDFANRFVGGGVTGAGLVQEEIRFLINPELIVSRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWARSHEDGSEKDDWQRRCTEIVAIDALHFRRYLDQFVPEKVRRELNKAYCGFLRPGVPSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELmRDIYSmHTFLTERKLDVGKVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVES 955
                                   453|  |   463       473       483       493       503  |    513  ||   530       540       550       560       570       580       590       600       610 |     620       630       640       650       660       670       680       690       700       710       720     | 730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900|     |910       920       930       940       950     
                                    454-MSE                                             506-MSE   516|                                                               590-MSE               612-MSE |                                                                                                         726-MSE                                                                                                                                                                        901-MSE |                                                
                                       457-MSE                                                     524                                                                                           618-MSE                                                                                                                                                                                                                                                                                          907-MSE                                            


Chain B from PDB  Type:PROTEIN  Length:494
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.......hhhhhh...........eee........................................hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh............eeeeeehhhhhhhhhhhhh.....................hhhhh.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh......eeee...hhhhhh...eeeee..............hhhhhhhhhhhhhhhhhhh.......eeeeeee....eeee......eeeee............eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh....hhhhh..eeee.........hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4na4 B 446 WLGTPIEEmRKmPRCGIHLPSLRPSASHTVTVRVDLLRAGEVPKPFPTHYKDLWDNKHVKmPCSEQNLYGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALVDFWDAEAQHLYQSILPDmVKIALCLPNICTQPIPLLKQKmNHSVTmSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEGNGRGmLQVDFANRFVGGGVTGAGLVQEEIRFLINPELIVSRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWARSHEDGSEKDDWQRRCTEIVAIDALHFRRYLDQFVPEKVRRELNKAYCGFLRPGVPSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELmRDIYSmHTFLTERKLDVGKVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVES 955
                                   455 |     465       475       485       495       505|      526       536       546       556       566    || 581       591       601       611|     |621       631       641       651       661       671       681       691       701       711       721    |  731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901     | 911       921       931       941       951    
                                  454-MSE                                             506-MSE 514|                                          571|          590-MSE               612-MSE |                                                                                                         726-MSE                                                                                                                                                                        901-MSE |                                                
                                     457-MSE                                                   526                                           577                                      618-MSE                                                                                                                                                                                                                                                                                          907-MSE                                            


Chain C from PDB  Type:PROTEIN  Length:505
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhh..................eee.....................................ee...eehhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeehhhhhhhhhhhhh.....................hhhhhh....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh......eeee...hhhhhh...eeeee..............hhhhhhhhhhhhhhhhhhh.......eeeeee.....eeee.hhhhheeeee...............eeeee......hhhhhhhhhhhhhhhhhhhhhhh....hhhhh..eee..........hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4na4 C 444 KKWLGTPIEEmRKmPRCGIHLPSLRPSASHTVTVRVDLLRAGEVPKPFPTHYKDLWDNKHVKmPCSEQNLYPTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALVDFWDKVLEEAEAQHLYQSILPDmVKIALCLPNICTQPIPLLKQKmNHSVTmSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEGNGRGmLQVDFANRFVGGGVTGAGLVQEEIRFLINPELIVSRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWARSHEDGSEKDDWQRRCTEIVAIDALHFRRYLDQFVPEKVRRELNKAYCGFLRPGVPSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELmRDIYSmHTFLTERKLDVGKVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESS 956
                                   453|  |   463       473       483       493       503  |    513 ||    531       541       551       561       571       581       591       601       611|     |621       631       641       651       661       671       681       691       701       711       721    |  731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901     | 911       921       931       941       951     
                                    454-MSE                                             506-MSE  515|                                                               590-MSE               612-MSE |                                                                                                         726-MSE                                                                                                                                                                        901-MSE |                                                 
                                       457-MSE                                                    524                                                                                           618-MSE                                                                                                                                                                                                                                                                                          907-MSE
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  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 4NA4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NA4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NA4)

(-) Gene Ontology  (10, 10)

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  3.2.1.143
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 Related Entries

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

UniProtKB/Swiss-Prot
        PARG_MOUSE | O88622: 4fc2 4n9y 4n9z 4na0 4na5 4na6

(-) Related Entries Specified in the PDB File

4fc2 WILD TYPE
4n9y E748Q
4n9z E749Q
4na0 WILD TYPE WITH ADPRIBOSE
4na5