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(-) Description

Title :  CRYSTAL STRUCTURE OF 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE (TM1009) FROM THERMOTOGA MARITIMA AT 2.40 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  13 Oct 04  (Deposition) - 26 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tm1009, 2, 5-Diketo-D-Gluconic Acid Reductase (Ec 1. 1. 1. 274), Structural Genomics, Joint Center For Structural Genomics, Jcsg, Psi, Protein Structure Initiative, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of 2, 5-Diketo-D-Gluconic Acid Reductase (Tm1009) From Thermotoga Maritima At 2. 40 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE
    Chains: A, B
    EC Number: 1.1.1.274
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1009
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:20 , VAL A:21 , PHE A:22 , ASP A:45 , TYR A:50 , HIS A:112 , SER A:140 , ASN A:141 , GLN A:162 , TRP A:188 , GLY A:189 , PRO A:190 , PHE A:191 , ALA A:192 , GLU A:193 , PHE A:199 , ALA A:216 , ILE A:231 , PRO A:232 , LYS A:233 , THR A:234 , VAL A:235 , ARG A:239 , GLU A:242 , ASN A:243 , HOH A:359 , HOH A:401BINDING SITE FOR RESIDUE NAP A 300
2AC2SOFTWAREGLY B:20 , VAL B:21 , PHE B:22 , ASP B:45 , TYR B:50 , SER B:140 , ASN B:141 , GLN B:162 , TRP B:188 , GLY B:189 , PRO B:190 , PHE B:191 , ALA B:192 , GLU B:193 , PHE B:199 , ALA B:216 , ILE B:231 , PRO B:232 , LYS B:233 , THR B:234 , VAL B:235 , ARG B:236 , ARG B:239 , GLU B:242 , ASN B:243 , HOH B:324 , HOH B:374BINDING SITE FOR RESIDUE NAP B 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VP5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VP5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VP5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VP5)

(-) Exons   (0, 0)

(no "Exon" information available for 1VP5)

(-) 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:284
 aligned with Q9X0A2_THEMA | Q9X0A2 from UniProtKB/TrEMBL  Length:286

    Alignment length:284
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281    
         Q9X0A2_THEMA     2 QVPKVTLNNGVEMPILGYGVFQIPPEKTEECVYEAIKVGYRLIDTAASYMNEEGVGRAIKRAIDEGIVRREELFVTTKLWVSDVGYESTKKAFEKSLKKLQLEYIDLYLIHQPFGDVHCAWKAMEEMYKDGLVRAIGVSNFYPDRLMDLMVHHEIVPAVNQIEIHPFYQRQEEIEFMRNYNIQPEAWGPFAEGRKNIFQNGVLRSIAEKYGKTVAQVILRWLTQKGIVAIPKTVRRERMKENISIFDFELTQEDMEKIATLDEGQSAFFSHRDPEVVKWICSLK 285
               SCOP domains d1vp5a_ A: 2,5-diketo-D-gluconic acid reductase A                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1vp5A00 A:2-285 NADP-dependent oxidoreductase                                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.....eee...ee....hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh...hhhhheeeeeehhhhh.hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh............hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vp5 A   2 QVPKVTLNNGVEMPILGYGVFQIPPEKTEECVYEAIKVGYRLIDTAASYMNEEGVGRAIKRAIDEGIVRREELFVTTKLWVSDVGYESTKKAFEKSLKKLQLEYIDLYLIHQPFGDVHCAWKAMEEMYKDGLVRAIGVSNFYPDRLMDLMVHHEIVPAVNQIEIHPFYQRQEEIEFMRNYNIQPEAWGPFAEGRKNIFQNGVLRSIAEKYGKTVAQVILRWLTQKGIVAIPKTVRRERMKENISIFDFELTQEDMEKIATLDEGQSAFFSHRDPEVVKWICSLK 285
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281    


Chain B from PDB  Type:PROTEIN  Length:283
 aligned with Q9X0A2_THEMA | Q9X0A2 from UniProtKB/TrEMBL  Length:286

    Alignment length:283
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281   
         Q9X0A2_THEMA     2 QVPKVTLNNGVEMPILGYGVFQIPPEKTEECVYEAIKVGYRLIDTAASYMNEEGVGRAIKRAIDEGIVRREELFVTTKLWVSDVGYESTKKAFEKSLKKLQLEYIDLYLIHQPFGDVHCAWKAMEEMYKDGLVRAIGVSNFYPDRLMDLMVHHEIVPAVNQIEIHPFYQRQEEIEFMRNYNIQPEAWGPFAEGRKNIFQNGVLRSIAEKYGKTVAQVILRWLTQKGIVAIPKTVRRERMKENISIFDFELTQEDMEKIATLDEGQSAFFSHRDPEVVKWICSL 284
               SCOP domains d1vp5b_ B: 2,5-diketo-D-gluconic acid reductase A                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1vp5B00 B:2-284 NADP-dependent oxidoreductase                                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) --------------Aldo_ket_red-1vp5B01 B:16-264                                                                                                                                                                                                                            -------------------- Pfam domains (1)
           Pfam domains (2) --------------Aldo_ket_red-1vp5B02 B:16-264                                                                                                                                                                                                                            -------------------- Pfam domains (2)
         Sec.struct. author ...eee.....eee...ee....hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh...hhhhheeeeeehhhhh.hhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh............hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vp5 B   2 QVPKVTLNNGVEMPILGYGVFQIPPEKTEECVYEAIKVGYRLIDTAASYMNEEGVGRAIKRAIDEGIVRREELFVTTKLWVSDVGYESTKKAFEKSLKKLQLEYIDLYLIHQPFGDVHCAWKAMEEMYKDGLVRAIGVSNFYPDRLMDLMVHHEIVPAVNQIEIHPFYQRQEEIEFMRNYNIQPEAWGPFAEGRKNIFQNGVLRSIAEKYGKTVAQVILRWLTQKGIVAIPKTVRRERMKENISIFDFELTQEDMEKIATLDEGQSAFFSHRDPEVVKWICSL 284
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281
   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: Aldo_ket_red] (94)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9X0A2_THEMA | Q9X0A2)
molecular function
    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.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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