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(-) Description

Title :  GEOBACILLUS STEAROTHERMOPHILUS 6-PHOSPHOGLUCONATE DEHYDROGENASE WITH BOUND 6-PHOSPHOGLUCONATE
 
Authors :  S. Cameron, V. P. Martini, J. Iulek, W. N. Hunter
Date :  20 Jan 09  (Deposition) - 07 Apr 09  (Release) - 16 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  6Pdh, Geobacillus, Dehydrogenase, Phsophogluconate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Cameron, V. P. Martini, J. Iulek, W. N. Hunter
Geobacillus Stearothermophilus 6-Phosphogluconate Dehydrogenase, Complexed With 6-Phosphogluconate.
Acta Crystallogr. , Sect. F V. 65 450 2009
PubMed-ID: 19407374  |  Reference-DOI: 10.1107/S1744309109012767

(-) Compounds

Molecule 1 - 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
    Atcc: 12980
    Chains: A, B
    EC Number: 1.1.1.44
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B MODIFIED TO CONTAIN TEV CLEAVAGE SITE
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 469008
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Other Details: ATCC/LGC-BIOCHEM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
16PG1Ligand/Ion6-PHOSPHOGLUCONIC ACID
2SO42Ligand/IonSULFATE ION
3TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:102 , SER A:128 , GLY A:129 , GLY A:130 , LYS A:182 , HIS A:185 , ASN A:186 , GLU A:189 , TYR A:190 , GLN A:259 , LYS A:260 , ARG A:287 , HOH A:2109 , HOH A:2177 , HOH A:2371 , HOH A:2372 , HOH A:2373 , HOH A:2374 , HOH A:2375 , HOH A:2376 , ARG B:446 , HIS B:452BINDING SITE FOR RESIDUE 6PG A 500
2AC2SOFTWAREARG A:446 , HIS A:452 , HOH A:2348 , HOH A:2352 , HOH A:2377 , GLY B:258 , HOH B:2224BINDING SITE FOR RESIDUE TRS A 501
3AC3SOFTWAREGLY A:258 , GLN A:259 , LYS A:260 , ARG B:446 , HIS B:452BINDING SITE FOR RESIDUE TRS A 502
4AC4SOFTWAREARG A:446 , HIS A:452 , TYR B:190 , GLN B:259 , LYS B:260 , ARG B:287 , HOH B:2173 , HOH B:2174 , HOH B:2373 , HOH B:2374BINDING SITE FOR RESIDUE SO4 B 500
5AC5SOFTWARESER B:128 , GLY B:129 , GLY B:130 , LYS B:182 , HIS B:185 , GLU B:189 , ILE B:366 , HOH B:2135 , HOH B:2174 , HOH B:2373 , HOH B:2375BINDING SITE FOR RESIDUE SO4 B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W90)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:66 -Pro A:67
2Lys B:66 -Pro B:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W90)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W90)

(-) Exons   (0, 0)

(no "Exon" information available for 2W90)

(-) 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:470
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d2w90a1 A:0-175 automated matches                                                                                                                                               d2w90a2 A:176-469 automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2w90A01 A:0-179 NAD(P)-binding Rossmann-like Domain                                                                                                                                 2w90A02 A:180-435 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                                                                                                                     2w90A03 A:436-469                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh...eee..hhhhhhhh.....eeee....hhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhh.eeeeeehhhhhhhhhhhhhhhh.ee..ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhh..........hhhh...........hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w90 A   0 HMAKHQIGVIGLAVMGKNLALNIESKGYSVAVYNRLREKTDEFLQEAKGKNIVGTYSIEEFVNALEKPRKILLMVKAGAPTDATIEQLKPHLEKGDIVIDGGNTYFKDTQRRNKELAELGIHFIGTGVSGGEEGALKGPSIMPGGQKEAHELVRPIFEAIAAKVDGEPCTTYIGPDGAGHYVKMVHNGIEYGDMQLIAEAYFLLKHVLGMDAAELHEVFADWNKGELNSYLIEITADIFTKIDEETGKPLVDVILDKAGQKGTGKWTSQNALDLGVPLPIITESVFARFLSAMKDERVKASKVLAGPAVKPFEGDRAHFIEAVRRALYMSKICSYAQGFAQMKAASEEYNWNLRYGDIAMIFRGGCIIRAQFLQKIKEAYDRDPALSNLLLDSYFKDIVERYQDALREIVATAAMRGIPVPGSASALAYYDSYRTAVLPANLIQAQRDYFGAHTYERVDKEGIFHTEWLK 469
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469


Chain B from PDB  Type:PROTEIN  Length:471
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d2w90b1 B:-1-175 automated matches                                                                                                                                               d2w90b2 B:176-469 automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2w90B01 B:-1-179 NAD(P)-binding Rossmann-like Domain                                                                                                                                 2w90B02 B:180-435 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                                                                                                                     2w90B03 B:436-469                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh....eee..hhhhhhhh.....eeee....hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh...eeeeeeeehhhhhhhhh.eeeeeehhhhhhhhhhhhhhhh.ee..ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhhhhhhh.........hhhhhh..........hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..ee......ee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w90 B  -1 GHMAKHQIGVIGLAVMGKNLALNIESKGYSVAVYNRLREKTDEFLQEAKGKNIVGTYSIEEFVNALEKPRKILLMVKAGAPTDATIEQLKPHLEKGDIVIDGGNTYFKDTQRRNKELAELGIHFIGTGVSGGEEGALKGPSIMPGGQKEAHELVRPIFEAIAAKVDGEPCTTYIGPDGAGHYVKMVHNGIEYGDMQLIAEAYFLLKHVLGMDAAELHEVFADWNKGELNSYLIEITADIFTKIDEETGKPLVDVILDKAGQKGTGKWTSQNALDLGVPLPIITESVFARFLSAMKDERVKASKVLAGPAVKPFEGDRAHFIEAVRRALYMSKICSYAQGFAQMKAASEEYNWNLRYGDIAMIFRGGCIIRAQFLQKIKEAYDRDPALSNLLLDSYFKDIVERYQDALREIVATAAMRGIPVPGSASALAYYDSYRTAVLPANLIQAQRDYFGAHTYERVDKEGIFHTEWLK 469
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2W90)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2W90)

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    Lys A:66 - Pro A:67   [ RasMol ]  
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  2w90
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(-) Related Entries Specified in the PDB File

2w8z GEOBACILLUS STEAROTHERMOPHILUS 6-PHOSPHOGLUCONATE WITH BOUND 6-PHOSPHOGLUCONATE