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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE POLY(ADP-RIBOSE) GLYCOHYDROLASE (PARG) CATALYTIC DOMAIN MUTANT E749N
 
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 :  2.48
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (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
    EC Number: 3.2.1.143
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CATALYTIC DOMAIN
    Gene: PARG
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:444 , LEU A:447 , ARG A:902BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREARG A:656 , ARG A:664 , LYS A:665 , LYS A:668 , GLY A:744BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWAREARG A:528 , TYR A:557 , PRO A:636 , ARG A:637 , ASN A:639BINDING SITE FOR RESIDUE SO4 A 1003
4AC4SOFTWAREPRO A:465 , SER A:466 , ARG A:468BINDING SITE FOR RESIDUE SO4 A 1004
5AC5SOFTWARELYS B:444 , LEU B:447 , ARG B:902BINDING SITE FOR RESIDUE SO4 B 1001
6AC6SOFTWAREARG B:656 , ARG B:664 , LYS B:665 , LYS B:668 , GLY B:744BINDING SITE FOR RESIDUE SO4 B 1002
7AC7SOFTWAREARG B:528 , TYR B:557 , PRO B:636 , ARG B:637 , ASN B:639BINDING SITE FOR RESIDUE SO4 B 1003
8AC8SOFTWAREPRO B:465 , SER B:466 , ARG B:468BINDING SITE FOR RESIDUE SO4 B 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NA6)

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NA6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NA6)

(-) Exons   (0, 0)

(no "Exon" information available for 4NA6)

(-) 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:507
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhhhh..................eee.....................................ee..eehhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeehhhhhhhhhhhhh....................hhhhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeeeee................eeee...hhhhhh...eeeee..............hhhhhhhhhhhhhhhhhhhh......eeeeeee....eeee.hhhhheeeee............eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh....hhhhh..eee....hhhhh.hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4na6 A 442 PEKKWLGTPIEEMRKMPRCGIHLPSLRPSASHTVTVRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALVDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLKQKMNHSVTMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEGNGRGMLQVDFANRFVGGGVTGAGLVQENIRFLINPELIVSRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWARSHEDGSEKDDWQRRCTEIVAIDALHFRRYLDQFVPEKVRRELNKAYCGFLRPGVPSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHTFLTERKLDVGKVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESSA 957
                                   451       461       471       481       491       501       511   ||  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       
                                                                                                   515|                                                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                    525                                                                                                                                                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:504
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee.hhhhh..................eee..hhhhh.................................hhhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeehhhhhhhhhhhhh....................hhhhhh....hhhhhhhhhhhhhhhhhhhh....eeeeeeee................eeee...hhhhhh...eeeeee.............hhhhhhhhhhhhhhhhhhh.......eeeeee.....eeee.hhhhheeeee...............eeeeee.....hhhhhhhhhhhhhhhhhhhhhhh....hhhhh..eeee...hhhhh.hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4na6 B 443 EKKWLGTPIEEMRKMPRCGIHLPSLRPSASHTVTVRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALVDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLKQKMNHSVTMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEGNGRGMLQVDFANRFVGGGVTGAGLVQENIRFLINPELIVSRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWARSHEDGSEKDDWQRRCTEIVAIDALHFRRYLDQFVPEKVRRELNKAYCGFLRPGVPSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHTFLTERKLDVGKVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESSA 957
                                   452       462       472       482       492       502       512 ||    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       943       953    
                                                                                                 514|                                                                                                                                                                                                                                                                                                                                                                                                                                               
                                                                                                  526
   Legend:   → Mismatch (orange background)
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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 4NA6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NA6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NA6)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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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 4na4 4na5

(-) Related Entries Specified in the PDB File

4fc2 WILD TYPE
4n9y E748Q
4n9z E749Q
4na0 WILD TYPE WITH ADPRIBOSE
4na4 WILD TYPE WITH ADP-HPD
4na5 E748N