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(-) Description

Title :  CRYSTAL STRUCTURE OF A PREDICTED OXALATE DECARBOXYLASE (TM1287) FROM THERMOTOGA MARITIMA AT 1.95 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  03 Jul 03  (Deposition) - 15 Jul 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Double-Stranded Beta-Helix Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Schwarzenbacher, F. Von Delft, L. Jaroszewski, P. Abdubek, E. Ambing, T. Biorac, L. S. Brinen, J. M. Canaves, J. Cambell, H. J. Chiu X. Dai, A. M. Deacon, M. Didonato, M. A. Elsliger, S. Eshagi, R. Floyd, A. Godzik, C. Grittini, S. K. Grzechnik, E. Hampton, C. Karlak, H. E. Klock, E. Koesema, J. S. Kovarik, A. Kreusch, P. Kuhn, S. A. Lesley I. Levin, D. Mcmullan, T. M. Mcphillips, M. D. Miller, A. Morse, K. Moy, J. Ouyang, R. Page, K. Quijano, A. Robb, G. Spraggon, R. C. Stevens, H. Van Den Bedem, J. Velasquez, J. Vincent, X. Wang, B. West, G. Wolf, Q. Xu, K. O. Hodgson, J. Wooley, I. A. Wilson
Crystal Structure Of A Putative Oxalate Decarboxylase (Tm1287) From Thermotoga Maritima At 1. 95 A Resolution
Proteins V. 56 392 2004
PubMed-ID: 15211523  |  Reference-DOI: 10.1002/PROT.20016

(-) Compounds

Molecule 1 - PUTATIVE OXALATE DECARBOXYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1287
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2OXL2Ligand/IonOXALATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:61 , HIS A:63 , GLU A:68 , HIS A:102 , OXL A:400BINDING SITE FOR RESIDUE MN A 300
2AC2SOFTWAREHIS B:61 , HIS B:63 , GLU B:68 , HIS B:102 , OXL B:401BINDING SITE FOR RESIDUE MN B 301
3AC3SOFTWAREHIS A:61 , HIS A:63 , GLU A:68 , TYR A:70 , HIS A:102 , MN A:300 , HOH A:491BINDING SITE FOR RESIDUE OXL A 400
4AC4SOFTWAREARG B:23 , HIS B:61 , HIS B:63 , GLU B:68 , TYR B:70 , HIS B:102 , ILE B:118 , MN B:301 , HOH B:506BINDING SITE FOR RESIDUE OXL B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O4T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O4T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O4T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1O4T)

(-) Exons   (0, 0)

(no "Exon" information available for 1O4T)

(-) 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:115
 aligned with OXBP_THEMA | Q9X113 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:115
                                    16        26        36        46        56        66        76        86        96       106       116     
           OXBP_THEMA     7 MVVRSSEITPERISNMRGGKGEVEMAHLLSKEAMHNKARLFARMKLPPGSSVGLHKHEGEFEIYYILLGEGVFHDNGKDVPIKAGDVCFTDSGESHSIENTGNTDLEFLAVIILL 121
               SCOP domains d1o4ta_ A: Hypothetical protein TM1287                                                                              SCOP domains
               CATH domains 1o4tA00 A:7-121 Jelly Rolls                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhh..eeee.......eeeeee..........eeeeeeeee....eeeeee...eeeeeeeee.eeeeee..eeeeee..eeeee....eeeee......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1o4t A   7 MVVRSSEITPERISNMRGGKGEVEMAHLLSKEAMHNKARLFARMKLPPGSSVGLHKHEGEFEIYYILLGEGVFHDNGKDVPIKAGDVCFTDSGESHSIENTGNTDLEFLAVIILL 121
                                    16        26        36        46        56        66        76        86        96       106       116     


Chain B from PDB  Type:PROTEIN  Length:115
 aligned with OXBP_THEMA | Q9X113 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:115
                                    16        26        36        46        56        66        76        86        96       106       116     
           OXBP_THEMA     7 MVVRSSEITPERISNMRGGKGEVEMAHLLSKEAMHNKARLFARMKLPPGSSVGLHKHEGEFEIYYILLGEGVFHDNGKDVPIKAGDVCFTDSGESHSIENTGNTDLEFLAVIILL 121
               SCOP domains d1o4tb_ B: Hypothetical protein TM1287                                                                              SCOP domains
               CATH domains 1o4tB00 B:7-121 Jelly Rolls                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhh..eeee.......eeeeee..........eeeeeeeee....eeeeee...eeeeeeeee.eeeeee..eeeeee..eeeee....eeeee......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1o4t B   7 MVVRSSEITPERISNMRGGKGEVEMAHLLSKEAMHNKARLFARMKLPPGSSVGLHKHEGEFEIYYILLGEGVFHDNGKDVPIKAGDVCFTDSGESHSIENTGNTDLEFLAVIILL 121
                                    16        26        36        46        56        66        76        86        96       106       116
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  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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1O4T)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (OXBP_THEMA | Q9X113)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0046564    oxalate decarboxylase activity    Catalysis of the reaction: H(+) + oxalate = CO(2) + formate.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0033609    oxalate metabolic process    The chemical reactions and pathways involving oxalate, the organic acid ethanedioate.

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