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(-) Description

Title :  STRUCTURE OF TT0495 PROTEIN FROM THERMUS THERMOPHILUS
 
Authors :  N. K. Lokanath, K. J. Pampa, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  23 Mar 07  (Deposition) - 01 Apr 08  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  A,C  (1x)
Biol. Unit 5:  B,D  (1x)
Keywords :  Gluconate Dehydrogenase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Pampa, N. K. Lokanath, N. Kunishima, R. V. Rai
The First Crystal Structure Of Nad-Dependent 3-Dehydro-2-Deoxy-D-Gluconate Dehydrogenase From Thermus Thermophilus Hb8
Acta Crystallogr. , Sect. D V. 70 994 2014
PubMed-ID: 24699644  |  Reference-DOI: 10.1107/S1399004713034925

(-) Compounds

Molecule 1 - 2-DEOXY-D-GLUCONATE 3-DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.125
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: GLUCONATE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x):   CD
Biological Unit 4 (1x): A C 
Biological Unit 5 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO49Ligand/IonSULFATE ION
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO49Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 4 (2, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
Biological Unit 5 (2, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO45Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:12 , GLY B:13 , THR B:179 , GLU B:180 , HOH B:2089 , HOH B:2187 , HOH B:2188 , HOH B:2189 , HOH C:2022 , HOH C:2053BINDING SITE FOR RESIDUE SO4 B 2001
02AC2SOFTWAREARG A:12 , GLY A:13 , GLU A:180 , HOH A:2067 , HOH A:2231BINDING SITE FOR RESIDUE SO4 A 2002
03AC3SOFTWAREGLY C:13 , THR C:179 , GLU C:180 , HOH C:2193 , HOH C:2264BINDING SITE FOR RESIDUE SO4 C 2003
04AC4SOFTWAREGLY B:128 , SER B:129 , TYR B:144 , LYS B:148 , PRO B:174 , HOH B:2085 , HOH B:2220 , HOH B:2259BINDING SITE FOR RESIDUE SO4 B 2004
05AC5SOFTWARESER A:90 , TYR A:91 , HOH A:2241 , GLN B:110 , HOH B:2263 , HOH B:2264BINDING SITE FOR RESIDUE SO4 B 2005
06AC6SOFTWAREGLN A:110 , SER B:90 , TYR B:91 , HOH B:2177 , HOH B:2229BINDING SITE FOR RESIDUE SO4 B 2006
07AC7SOFTWARELEU C:89 , SER C:90 , TYR C:91 , HOH C:2224 , HOH C:2276 , HOH C:2280 , GLN D:110BINDING SITE FOR RESIDUE SO4 C 2007
08AC8SOFTWARELEU C:107 , GLN C:110 , HOH C:2211 , HOH C:2212 , SER D:90 , TYR D:91BINDING SITE FOR RESIDUE SO4 C 2008
09AC9SOFTWARESER B:11 , SER B:33 , ARG B:34 , HOH B:2121 , HOH B:2266 , HOH B:2267 , HOH B:2268 , GLU C:92BINDING SITE FOR RESIDUE SO4 B 2009
10BC1SOFTWARESER B:129 , ILE B:141 , LEU B:185 , HOH B:2019 , HOH B:2085BINDING SITE FOR RESIDUE GOL B 1287
11BC2SOFTWARESER A:129 , PRO A:174 , GLY A:175BINDING SITE FOR RESIDUE GOL A 1288

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EKQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2EKQ)

(-) 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:238
 aligned with Q53W82_THET8 | Q53W82 from UniProtKB/TrEMBL  Length:239

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
         Q53W82_THET8     2 ERKALVTGGSRGIGRAIAEALVARGYRVAIASRNPEEAAQSLGAVPLPTDLEKDDPKGLVKRALEALGGLHVLVHAAAVNVRKPALELSYEEWRRVLYLHLDVAFLLAQAAAPHMAEAGWGRVLFIGSVTTFTAGGPVPIPAYTTAKTALLGLTRALAKEWARLGIRVNLLCPGYVETEFTLPLRQNPELYEPITARIPMGRWARPEEIARVAAVLCGDEAEYLTGQAVAVDGGFLAY 239
               SCOP domains d2ekqa_ A: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2ekqA00 A:2-239 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee..hhhhhhhhh.eeee......hhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ekq A   2 ERKALVTGGSRGIGRAIAEALVARGYRVAIASRNPEEAAQSLGAVPLPTDLEKDDPKGLVKRALEALGGLHVLVHAAAVNVRKPALELSYEEWRRVLYLHLDVAFLLAQAAAPHMAEAGWGRVLFIGSVTTFTAGGPVPIPAYTTAKTALLGLTRALAKEWARLGIRVNLLCPGYVETEFTLPLRQNPELYEPITARIPMGRWARPEEIARVAAVLCGDEAEYLTGQAVAVDGGFLAY 239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with Q53W82_THET8 | Q53W82 from UniProtKB/TrEMBL  Length:239

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
         Q53W82_THET8     2 ERKALVTGGSRGIGRAIAEALVARGYRVAIASRNPEEAAQSLGAVPLPTDLEKDDPKGLVKRALEALGGLHVLVHAAAVNVRKPALELSYEEWRRVLYLHLDVAFLLAQAAAPHMAEAGWGRVLFIGSVTTFTAGGPVPIPAYTTAKTALLGLTRALAKEWARLGIRVNLLCPGYVETEFTLPLRQNPELYEPITARIPMGRWARPEEIARVAAVLCGDEAEYLTGQAVAVDGGFLAY 239
               SCOP domains d2ekqb_ B: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2ekqB00 B:2-239 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee..hhhhhhhhh.eeee......hhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ekq B   2 ERKALVTGGSRGIGRAIAEALVARGYRVAIASRNPEEAAQSLGAVPLPTDLEKDDPKGLVKRALEALGGLHVLVHAAAVNVRKPALELSYEEWRRVLYLHLDVAFLLAQAAAPHMAEAGWGRVLFIGSVTTFTAGGPVPIPAYTTAKTALLGLTRALAKEWARLGIRVNLLCPGYVETEFTLPLRQNPELYEPITARIPMGRWARPEEIARVAAVLCGDEAEYLTGQAVAVDGGFLAY 239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        


Chain C from PDB  Type:PROTEIN  Length:238
 aligned with Q53W82_THET8 | Q53W82 from UniProtKB/TrEMBL  Length:239

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
         Q53W82_THET8     2 ERKALVTGGSRGIGRAIAEALVARGYRVAIASRNPEEAAQSLGAVPLPTDLEKDDPKGLVKRALEALGGLHVLVHAAAVNVRKPALELSYEEWRRVLYLHLDVAFLLAQAAAPHMAEAGWGRVLFIGSVTTFTAGGPVPIPAYTTAKTALLGLTRALAKEWARLGIRVNLLCPGYVETEFTLPLRQNPELYEPITARIPMGRWARPEEIARVAAVLCGDEAEYLTGQAVAVDGGFLAY 239
               SCOP domains d2ekqc_ C: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2ekqC00 C:2-239 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee..hhhhhhhhh.eeee......hhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ekq C   2 ERKALVTGGSRGIGRAIAEALVARGYRVAIASRNPEEAAQSLGAVPLPTDLEKDDPKGLVKRALEALGGLHVLVHAAAVNVRKPALELSYEEWRRVLYLHLDVAFLLAQAAAPHMAEAGWGRVLFIGSVTTFTAGGPVPIPAYTTAKTALLGLTRALAKEWARLGIRVNLLCPGYVETEFTLPLRQNPELYEPITARIPMGRWARPEEIARVAAVLCGDEAEYLTGQAVAVDGGFLAY 239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        


Chain D from PDB  Type:PROTEIN  Length:228
 aligned with Q53W82_THET8 | Q53W82 from UniProtKB/TrEMBL  Length:239

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
         Q53W82_THET8     2 ERKALVTGGSRGIGRAIAEALVARGYRVAIASRNPEEAAQSLGAVPLPTDLEKDDPKGLVKRALEALGGLHVLVHAAAVNVRKPALELSYEEWRRVLYLHLDVAFLLAQAAAPHMAEAGWGRVLFIGSVTTFTAGGPVPIPAYTTAKTALLGLTRALAKEWARLGIRVNLLCPGYVETEFTLPLRQNPELYEPITARIPMGRWARPEEIARVAAVLCGDEAEYLTGQAVAVDGGFLAY 239
               SCOP domains d2ekqd_ D: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2ekqD00 D:2-239 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee..hhhhhhhhh.eeee......hhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....----------.hhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ekq D   2 ERKALVTGGSRGIGRAIAEALVARGYRVAIASRNPEEAAQSLGAVPLPTDLEKDDPKGLVKRALEALGGLHVLVHAAAVNVRKPALELSYEEWRRVLYLHLDVAFLLAQAAAPHMAEAGWGRVLFIGSVTTFTAGGPVPIPAYTTAKTALLGLTRALAKEWARLGIRVNLLCPGYVET----------ELYEPITARIPMGRWARPEEIARVAAVLCGDEAEYLTGQAVAVDGGFLAY 239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       | -       191       201       211       221       231        
                                                                                                                                                                                                           179        190
   Legend:   → Mismatch (orange background)
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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  (1, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EKQ)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q53W82_THET8 | Q53W82)
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.

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  2ekq
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  Q53W82_THET8 | Q53W82
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  1.1.1.125
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 Related Entries

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

UniProtKB/TrEMBL
        Q53W82_THET8 | Q53W82: 1x1e 2ekp 4jp2 4jp3

(-) Related Entries Specified in the PDB File

2ekp THE SAME PROTEIN COMPLEXED WITH NAD RELATED ID: TTK003000495.3 RELATED DB: TARGETDB