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(-) Description

Title :  CRYSTAL STRUCTURE OF SURE PROTEIN FROM AQUIFEX AEOLICUS
 
Authors :  S. V. Antonyuk, M. J. Ellis, R. W. Strange, S. S. Hasnain, Y. Bessho, S. Kuramitsu, S. Yokoyama, Riken Structural Genomics Proteomics Initiative (Rsgi)
Date :  23 Aug 09  (Deposition) - 29 Sep 09  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Sure Protein, Putative Acid Phosphatase, Structural Genomics, 3-D Structure, Mixed Alpha/Beta Protein, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. V. Antonyuk, M. J. Ellis, R. W. Strange, Y. Bessho, S. Kuramitsu, A. Shinkai, S. Yokoyama, S. S. Hasnain
Structure Of Sure Protein From Aquifex Aeolicus Vf5 At 1. 5 A Resolution.
Acta Crystallogr. , Sect. F V. 65 1204 2009
PubMed-ID: 20054112  |  Reference-DOI: 10.1107/S1744309109043814

(-) Compounds

Molecule 1 - 5'-NUCLEOTIDASE SURE
    Chains: A, B
    EC Number: 3.1.3.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: CODONPLUS-RIL
    Expression System Vector Type: PLASMID
    Gene: SURE, AQ_832
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5
    Synonym: NUCLEOSIDE 5'-MONOPHOSPHATE PHOSPHOHYDROLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:9 , SER A:40 , ASN A:94 , ASN A:98 , SER A:106 , GLY A:107 , THR A:108 , NA A:254 , HOH A:2062 , HOH A:2164BINDING SITE FOR RESIDUE SO4 A 252
2AC2SOFTWAREASP A:10 , SER A:40 , ASN A:94 , SO4 A:252 , HOH A:2161BINDING SITE FOR RESIDUE NA A 254
3AC3SOFTWAREASP B:9 , SER B:40 , ASN B:94 , ASN B:98 , SER B:106 , GLY B:107 , THR B:108 , NA B:255 , HOH B:2289 , HOH B:2290 , HOH B:2291BINDING SITE FOR RESIDUE SO4 B 252
4AC4SOFTWAREASP B:10 , SER B:40 , ASN B:94 , SO4 B:252 , HOH B:2129BINDING SITE FOR RESIDUE NA B 255

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WQK)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:92 -Ile A:93
2Gly B:92 -Ile B:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WQK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WQK)

(-) Exons   (0, 0)

(no "Exon" information available for 2WQK)

(-) 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:248
 aligned with SURE_AQUAE | O67004 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        
           SURE_AQUAE     2 PTFLLVNDDGYFSPGINALREALKSLGRVVVVAPDRNLSGVGHSLTFTEPLKMRKIDTDFYTVIDGTPADCVHLGYRVILEEKKPDLVLSGINEGPNLGEDITYSGTVSGAMEGRILGIPSIAFSAFGRENIMFEEIAKVCVDIVKKVLNEGIPEDTYLNVNIPNLRYEEIKGIKVTRQGKRAYKERVFKYIDPYGKPFYWIAAEEFGWHAEEGTDYWAVLNGYVSVTPLHLDLTNYKVMKSIKYLED 249
               SCOP domains d2wqka_ A: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains 2wqkA00 A:2-249  [code=3.40.1210.10, no name defined]                                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..........hhhhhhhhh....eeeeee................eeeeeee..eeee...hhhhhhhh............eeeeeee......hhhhhh...............eeeeeee.....hhhhhhhhhhhhhhhhhhh.....eeeeeeee..hhhhh...ee........eeeeeeee.....eeeeeeee.........hhhhhhhh...eeeeee....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wqk A   2 PTFLLVNDDGYFSPGINALREALKSLGRVVVVAPDRNLSGVGHSLTFTEPLKMRKIDTDFYTVIDGTPADCVHLGYRVILEEKKPDLVLSGINEGPNLGEDITYSGTVSGAMEGRILGIPSIAFSAFGRENIMFEEIAKVCVDIVKKVLNEGIPEDTYLNVNIPNLRYEEIKGIKVTRQGKRAYKERVFKYIDPYGKPFYWIAAEEFGWHAEEGTDYWAVLNGYVSVTPLHLDLTNYKVMKSIKYLED 249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        


Chain B from PDB  Type:PROTEIN  Length:248
 aligned with SURE_AQUAE | O67004 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        
           SURE_AQUAE     2 PTFLLVNDDGYFSPGINALREALKSLGRVVVVAPDRNLSGVGHSLTFTEPLKMRKIDTDFYTVIDGTPADCVHLGYRVILEEKKPDLVLSGINEGPNLGEDITYSGTVSGAMEGRILGIPSIAFSAFGRENIMFEEIAKVCVDIVKKVLNEGIPEDTYLNVNIPNLRYEEIKGIKVTRQGKRAYKERVFKYIDPYGKPFYWIAAEEFGWHAEEGTDYWAVLNGYVSVTPLHLDLTNYKVMKSIKYLED 249
               SCOP domains d2wqkb_ B: automated matches                                                                                                                                                                                                                             SCOP domains
               CATH domains 2wqkB00 B:2-249  [code=3.40.1210.10, no name defined]                                                                                                                                                                                                    CATH domains
           Pfam domains (1) SurE-2wqkB01 B:2-188                                                                                                                                                                       ------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) SurE-2wqkB02 B:2-188                                                                                                                                                                       ------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eee..........hhhhhhhhh....eeeeee................eeeeeee..eeee...hhhhhhhh............eeeeeee......hhhhhh...............eeeeeee.....hhhhhhhhhhhhhhhhhhh.....eeeeeeee..hhhhh...ee........eeeeeeee.....eeeeeeee.........hhhhhhhh...eeeeee....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wqk B   2 PTFLLVNDDGYFSPGINALREALKSLGRVVVVAPDRNLSGVGHSLTFTEPLKMRKIDTDFYTVIDGTPADCVHLGYRVILEEKKPDLVLSGINEGPNLGEDITYSGTVSGAMEGRILGIPSIAFSAFGRENIMFEEIAKVCVDIVKKVLNEGIPEDTYLNVNIPNLRYEEIKGIKVTRQGKRAYKERVFKYIDPYGKPFYWIAAEEFGWHAEEGTDYWAVLNGYVSVTPLHLDLTNYKVMKSIKYLED 249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: SurE] (4)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SURE_AQUAE | O67004)
molecular function
    GO:0008253    5'-nucleotidase activity    Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008252    nucleotidase activity    Catalysis of the reaction: a nucleotide + H2O = a nucleoside + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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