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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE POLY(ADP-RIBOSE) GLYCOHYDROLASE (PARG) CATALYTIC DOMAIN MUTANT E749Q
 
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 :  1.90
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  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
2V3L2Ligand/Ion2'-O-(5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSYL)ADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
2V3L1Ligand/Ion2'-O-(5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSYL)ADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
2V3L1Ligand/Ion2'-O-(5-O-PHOSPHONO-ALPHA-D-RIBOFURANOSYL)ADENOSINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:469 , VAL A:475 , VAL A:477 , ARG A:478 , VAL A:479 , ASP A:480 , PHE A:491 , THR A:493 , HOH A:1112 , HOH A:1251 , HOH A:1416BINDING SITE FOR RESIDUE V3L A 1001
02AC2SOFTWAREARG A:824BINDING SITE FOR RESIDUE SO4 A 1002
03AC3SOFTWAREARG A:528 , PRO A:636 , ARG A:637 , ASN A:639 , HOH A:1237 , HOH A:1525BINDING SITE FOR RESIDUE SO4 A 1003
04AC4SOFTWARESER A:466 , ARG A:468 , HOH A:1191 , HOH A:1247BINDING SITE FOR RESIDUE SO4 A 1004
05AC5SOFTWAREARG A:656 , GLY A:739 , GLY A:742 , ALA A:743 , GLY A:744 , HOH A:1286BINDING SITE FOR RESIDUE SO4 A 1005
06AC6SOFTWAREARG A:637 , SER A:644 , GLU A:645 , HOH A:1257 , HOH A:1272BINDING SITE FOR RESIDUE SO4 A 1006
07AC7SOFTWAREPRO B:469 , VAL B:475 , VAL B:477 , ARG B:478 , VAL B:479 , ASP B:480 , PHE B:491 , THR B:493 , HOH B:1113 , HOH B:1457 , HOH B:1602 , HOH B:1607BINDING SITE FOR RESIDUE V3L B 1001
08AC8SOFTWAREARG B:824 , HOH B:1416 , HOH B:1613BINDING SITE FOR RESIDUE SO4 B 1002
09AC9SOFTWAREARG B:528 , PRO B:636 , ARG B:637 , ASN B:639 , HOH B:1167 , HOH B:1360BINDING SITE FOR RESIDUE SO4 B 1003
10BC1SOFTWAREPRO B:465 , SER B:466 , ARG B:468 , HOH B:1259 , HOH B:1405BINDING SITE FOR RESIDUE SO4 B 1004
11BC2SOFTWAREARG B:656 , GLY B:739 , GLY B:742 , ALA B:743 , GLY B:744 , HOH B:1556BINDING SITE FOR RESIDUE SO4 B 1005
12BC3SOFTWAREARG B:637 , LYS B:643 , SER B:644 , GLU B:645 , HOH B:1476 , HOH B:1579BINDING SITE FOR RESIDUE SO4 B 1006

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N9Z)

(-) 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 4N9Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N9Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4N9Z)

(-) 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:509
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               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...hhhhhhhhhhhhhhhhhhhh....eeeeeeee................eeee...hhhhhh...eeeeee.............hhhhhhhhhhhhhhhhhhhh......eeeeee.....eeee.hhhhheeeee...............eeeeee.....hhhhhhhhhhhhhhhhhhhhhhh....hhhhh..eeee...hhhhh.hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n9z A 442 PEKKWLGTPIEEMRKMPRCGIHLPSLRPSASHTVTVRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPVTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALVDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLKQKMNHSVTMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEGNGRGMLQVDFANRFVGGGVTGAGLVQEQIRFLINPELIVSRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWARSHEDGSEKDDWQRRCTEIVAIDALHFRRYLDQFVPEKVRRELNKAYCGFLRPGVPSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHTFLTERKLDVGKVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESSA 957
                                   451       461       471       481       491       501       511    || 528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948         
                                                                                                    516|                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                     524                                                                                                                                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:508
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhhhh..................eee..hhhhh..............................ee...eehhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeehhhhhhhhhhhhh.....................hhhhhh...hhhhhhhhhhhhhhhhhhhh....eeeeeeee................eeee...hhhhhh...eeeee..............hhhhhhhhhhhhhhhhhhhh......eeeeee.....eeee.hhhhheeeee...............eeeee......hhhhhhhhhhhhhhhhhhhhhhh....hhhhh..eeee...hhhhh.hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n9z B 442 PEKKWLGTPIEEMRKMPRCGIHLPSLRPSASHTVTVRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALVDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLKQKMNHSVTMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEGNGRGMLQVDFANRFVGGGVTGAGLVQEQIRFLINPELIVSRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWARSHEDGSEKDDWQRRCTEIVAIDALHFRRYLDQFVPEKVRRELNKAYCGFLRPGVPSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHTFLTERKLDVGKVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESSA 957
                                   451       461       471       481       491       501       511   ||  529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949        
                                                                                                   515|                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                    524
   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 4N9Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N9Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N9Z)

(-) 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 4na0 4na4 4na5 4na6

(-) Related Entries Specified in the PDB File

4fc2 WILD TYPE
4n9y E748Q
4na0
4na4
4na5
4na6