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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NUDIX DOMAIN OF NUDT6
 
Authors :  L. Tresaugues, M. Moche, C. H. Arrowsmith, H. Berglund, C. Bountra, R. C A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, A. Jo I. Johansson, T. Karlberg, T. Kotyenova, A. Kotzch, T. K. Nielsen, T. N C. Persson, J. Sagemark, H. Schueler, P. Schutz, M. I. Siponen, L. Sven A. G. Thorsell, S. Van Den Berg, J. Weigelt, M. Welin, M. Wisniewska, P. Nordlund, Structural Genomics Consortium (Sgc)
Date :  30 Apr 09  (Deposition) - 07 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Nudt6, Nudix, Hydrolase, Gfg, Gfg-1, Fgf2As, Structural Genomics, Structural Genomics Consortium, Sgc, Sgc Stockholm, Isopeptide Bond, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Tresaugues, M. Moche, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, A. Johansson, I. Johansson, T. Karlberg, T. Kotyenova, A. Kotzch, T. K. Nielsen, T. Nyman, C. Persson, J. Sagemark, H. Schueler, P. Schutz, M. I. Siponen, L. Svensson, A. G. Thorsell, S. Van Den Berg, J. Weigelt, M. Welin, M. Wisniewska, P. Nordlund
Crystal Structure Of The Nudix Domain Of Nudt6
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 6
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-BSA4
    Expression System Strain: BL21(DE3) R3 PRARE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 141-316
    Gene: FGF2AS, NUDT6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUDIX MOTIF 6, PROTEIN GFG, GFG-1, ANTISENSE BASIC FIBROBLAST GROWTH FACTOR

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1FLC2Ligand/IonCITRATE ANION
2GOL4Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGOL A:2 , LYS A:166 , LYS A:172 , ARG A:209 , THR A:261 , ALA A:291 , VAL A:292 , TYR A:293 , TYR A:298 , HOH A:1003 , HOH A:1038 , HOH A:1120 , HOH A:1129BINDING SITE FOR RESIDUE FLC A 1
2AC2SOFTWAREFLC A:1 , ALA A:147 , LYS A:172 , PHE A:173 , ARG A:209 , TYR A:224 , ILE A:263 , THR A:264BINDING SITE FOR RESIDUE GOL A 2
3AC3SOFTWAREGLU A:153 , SER A:154 , THR A:257 , GLU A:258 , THR A:260 , PRO A:262 , SER A:265 , TYR A:275 , HOH A:1034BINDING SITE FOR RESIDUE GOL A 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H95)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H95)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021909R209QNUDT6_HUMANPolymorphism1048201AR209Q
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021909R209QNUDT6_HUMANPolymorphism1048201AR209Q
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIX_BOXPS00893 Nudix box signature.NUDT6_HUMAN176-197  1A:176-197
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIX_BOXPS00893 Nudix box signature.NUDT6_HUMAN176-197  2A:176-197

(-) Exons   (0, 0)

(no "Exon" information available for 3H95)

(-) 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:161
 aligned with NUDT6_HUMAN | P53370 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:170
                                   152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
          NUDT6_HUMAN   143 QVGVAGAVFDESTRKILVVQDRNKLKNMWKFPGGLSEPEEDIGDTAVREVFEETGIKSEFRSVLSIRQQHTNPGAFGKSDMYIICRLKPYSFTINFCQEECLRCEWMDLNDLAKTENTTPITSRVARLLLYGYREGFDKIDLTVEELPAVYTGLFYKLYHKELPENYKTM 312
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....eeeeeee...........eee.....hhhhhhhhhhhhhhh..eeeeeeeeeee..---------.eeeeeeeee...........eeeeeeeehhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.eeeeeee......eeeeeee..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------Q------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------NUDIX_BOX             ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h95 A 143 QVGVAGAVFDESTRKILVVQDRNKLKNMWKFPGGLSEPEEDIGDTAVREVFEETGIKSEFRSVLSIRQQH---------DMYIICRLKPYSFTINFCQEECLRCEWMDLNDLAKTENTTPITSRVARLLLYGYREGFDKIDLTVEELPAVYTGLFYKLYHKELPENYKTM 312
                                   152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312
                                                                                               212       222
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3H95)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H95)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H95)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (NUDT6_HUMAN | P53370)
molecular function
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    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.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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

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        NUDT6_HUMAN | P53370: 3fxt

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