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(-) Description

Title :  STRUCTURE OF HUMAN PARG CATALYTIC DOMAIN IN COMPLEX WITH ADP-RIBOSE
 
Authors :  C. Brassington, J. Ellston, G. Hassall, G. Holdgate, M. Mcalister, G. S J. A. Tucker, M. Watson
Date :  10 Jul 12  (Deposition) - 19 Dec 12  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Tucker, N. Bennett, C. Brassington, S. T. Durant, G. Hassall, G. Holdgate, M. Mcalister, J. W. M. Nissink, C. Truman, M. Watson
Structures Of The Human Poly (Adp-Ribose) Glycohydrolase Catalytic Domain Confirm Catalytic Mechanism And Explain Inhibition By Adp-Hpd Derivatives.
Plos One V. 7 50889 2012
PubMed-ID: 23251397  |  Reference-DOI: 10.1371/JOURNAL.PONE.0050889

(-) Compounds

Molecule 1 - POLY(ADP-RIBOSE) GLYCOHYDROLASE
    ChainsA
    EC Number3.2.1.143
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A-6HIS
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantGOLD
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, RESIDUES 448-976
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric/Biological Unit (6, 9)
No.NameCountTypeFull Name
1AR62Ligand/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] HYDROGEN PHOSPHATE
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
4DTV1Ligand/Ion(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
5GOL2Ligand/IonGLYCEROL
6SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:603 , SER A:670 , PRO A:673BINDING SITE FOR RESIDUE BME A1603
2AC2SOFTWAREPRO A:706 , CYS A:711 , LYS A:713 , TYR A:849 , HOH A:2228BINDING SITE FOR RESIDUE DTV A1711
3AC3SOFTWAREASN A:740 , HIS A:828 , PHE A:875 , HOH A:2268BINDING SITE FOR RESIDUE GOL A1964
4AC4SOFTWAREGLU A:585 , HIS A:588 , LEU A:589 , HOH A:2203BINDING SITE FOR RESIDUE GOL A1965
5AC5SOFTWAREILE A:726 , GLU A:727 , PHE A:738 , ASN A:740 , GLY A:745 , VAL A:753 , GLN A:754 , GLU A:755 , GLU A:756 , TYR A:795 , ASN A:869 , GLY A:871 , CYS A:872 , GLY A:873 , ALA A:874 , PHE A:875 , PHE A:902 , HOH A:2265 , HOH A:2266 , HOH A:2301 , HOH A:2304 , HOH A:2339 , HOH A:2375 , HOH A:2376BINDING SITE FOR RESIDUE AR6 A1966
6AC6SOFTWAREPRO A:476 , VAL A:482 , ILE A:484 , ARG A:485 , VAL A:486 , ASP A:487 , PHE A:498 , HOH A:2032 , HOH A:2377BINDING SITE FOR RESIDUE AR6 A1967
7AC7SOFTWAREARG A:535 , TYR A:564 , PRO A:643 , ARG A:644 , ASN A:646 , ARG A:941 , ASN A:942 , HOH A:2166BINDING SITE FOR RESIDUE SO4 A1968
8AC8SOFTWARETRP A:506 , ARG A:644 , HOH A:2068BINDING SITE FOR RESIDUE SO4 A1969

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B1H)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Met A:464 -Pro A:465
2Phe A:498 -Pro A:499

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B1H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B1H)

(-) Exons   (0, 0)

(no "Exon" information available for 4B1H)

(-) Sequences/Alignments

Asymmetric/Biological 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
 aligned with PARG_HUMAN | Q86W56 from UniProtKB/Swiss-Prot  Length:976

    Alignment length:513
                                   460       470       480       490       500       510       520       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       960   
           PARG_HUMAN   451 KKWLGTPIEEMRRMPRCGIRLPLLRPSANHTVTIRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPVEDENGERTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALIDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLKQKMNHSITMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEENGQGMLQVDFANRFVGGGVTSAGLVQEEIRFLINPELIISRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWSRSHEDGSERDDWQRRCTEIVAIDALHFRRYLDQFVPEKMRRELNKAYCGFLRPGVSSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHIFLTERKLTVGDVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESC 963
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhh..................eee..hhhhh..............................eee.------..eeehhhhhhhhhh....hhhhhhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeehhhhhhhhhhhhh.....................hhhhhh....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....hhhhh......eeee...hhhhhh...eeeeee.............hhhhhhhhhhhhhhhhhhhh......eeeeee.....eeee.hhhhheeeee...............eeeeee.....hhhhhhhhhhhhhhhhhhhhhhh....hhhhh..eeee.........hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b1h A 451 KKWLGTPIEEMRRMPRcGIRLPLLRPSANHTVTIRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPV------RTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALIDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLAAAMNHSITMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTAAAPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEENGQGMLQVDFANRFVGGGVTSAGLVQEEIRFLINPELIISRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWSRSHEDGSERDDWQRRCTEIVAIDALHFRRYLDQFVPEKMRRELNKAYCGFLRPGVSSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHIFLTERKLTVGDVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESC 963
                                   460      |470       480       490       500       510       520  |    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       960   
                                          467-CSO                                                 523    530                                                                                                                                                                                                                                                                                                                                                                                                                                                 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4B1H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B1H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B1H)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PARG_HUMAN | Q86W56)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004649    poly(ADP-ribose) glycohydrolase activity    Catalysis of the hydrolysis of poly(ADP-ribose) at glycosidic (1''-2') linkage of ribose-ribose bond to produce free ADP-ribose.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PARG_HUMAN | Q86W564a0d 4b1g 4b1i 4b1j 5a7r 5lhb

(-) Related Entries Specified in the PDB File

4a0d STRUCTURE OF UNLIGANDED HUMAN PARG CATALYTIC DOMAIN
4b1g STRUCTURE OF UNLIGANDED HUMAN PARG CATALYTIC DOMAIN
4b1i STRUCTURE OF UNLIGANDED HUMAN PARG CATALYTIC DOMAIN
4b1j STRUCTURE OF UNLIGANDED HUMAN PARG CATALYTIC DOMAIN