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(-) Description

Title :  GEOBACILLUS STEAROTHERMOPHILUS 6-PHOSPHOGLUCONATE DEHYDROGENASE WITH BOUND 6-PHOSPHOGLUCONATE
 
Authors :  S. Cameron, W. N. Hunter
Date :  20 Jan 09  (Deposition) - 07 Apr 09  (Release) - 16 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, 6Pdh, Phsophogluconate, Dehydrogenase, Geobacillus (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
16PG2Ligand/Ion6-PHOSPHOGLUCONIC ACID
2SO41Ligand/IonSULFATE ION
3TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:14 , ASN A:102 , VAL A:127 , 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:2067 , HOH A:2070 , HOH A:2158 , HOH A:2159 , ARG B:446 , HIS B:452BINDING SITE FOR RESIDUE 6PG A1470
2AC2SOFTWARELYS A:256 , ALA A:291 , MET A:292 , LYS A:293 , ASP A:294 , HOH A:2160BINDING SITE FOR RESIDUE SO4 A1471
3AC3SOFTWAREARG A:446 , HIS A:452 , THR A:453 , HOH A:2161 , HOH A:2162 , HOH A:2163 , HOH A:2164 , HOH A:2165 , HOH A:2166 , HOH A:2167 , GLY B:258 , GLN B:259 , LYS B:260BINDING SITE FOR RESIDUE TRS A1472
4AC4SOFTWARESER A:345 , GLU A:346 , ASN A:349 , TRP A:350 , ASN A:351 , HOH A:2168BINDING SITE FOR RESIDUE TRS A1474
5AC5SOFTWAREARG A:446 , HIS A:452 , ASN B:102 , SER B:128 , GLY B:129 , GLY B:130 , LYS B:182 , HIS B:185 , ASN B:186 , GLU B:189 , TYR B:190 , GLN B:259 , LYS B:260 , THR B:262 , ARG B:287 , ILE B:366 , HOH B:2062 , HOH B:2172 , HOH B:2174 , HOH B:2175 , HOH B:2176 , HOH B:2177 , HOH B:2178 , HOH B:2179BINDING SITE FOR RESIDUE 6PG B1469

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W8Z)

(-) 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 2W8Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W8Z)

(-) Exons   (0, 0)

(no "Exon" information available for 2W8Z)

(-) 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:468
 aligned with I3NI58_GEOSE | I3NI58 from UniProtKB/TrEMBL  Length:470

    Alignment length:468
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462        
         I3NI58_GEOSE     3 AKHQIGVIGLAVMGKNLALNIESKGYSVAVYNRLREKTDEFLQEAKGKNIVGTYSIEEFVNALEKPRKILLMVKAGAPTDATIEQLKPHLEKGDIVIDGGNTYFKDTQRRNKELAELGIHFIGTGVSGGEEGALKGPSIMPGGQKEAHELVRPIFEAIAAKVDGEPCTTYIGPDGAGHYVKMVHNGIEYGDMQLIAEAYFLLKHVLGMDAAELHEVFADWNKGELNSYLIEITADIFTKIDEETGKPLVDVILDKAGQKGTGKWTSQNALDLGVPLPIITESVFARFLSAMKDERVKASKVLAGPAVKPFEGDRAHFIEAVRRALYMSKICSYAQGFAQMKAASEEYNWNLRYGDIAMIFRGGCIIRAQFLQKIKEAYDRDPALSNLLLDSYFKDIVERYQDALREIVATAAMRGIPVPGSASALAYYDSYRTAVLPANLIQAQRDYFGAHTYERVDKEGIFHTEWLK 470
               SCOP domains d2w8za1 A:2-175 automated matches                                                                                                                                             d2w8za2 A:176-469 automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2w8zA01 A:2-179 NAD(P)-binding Rossmann-like Domain                                                                                                                               2w8zA02 A:180-435 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                                                                                                                     2w8zA03 A:436-469                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhh....eeee..hhhhhhhhhhhh....eee..hhhhhhhh.....eeee....hhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhh.eeeeeehhhhhhhhhhhhhhhh.ee..ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhh..........hhhh...........hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2w8z A   2 AKHQIGVIGLAVMGKNLALNIESKGYSVAVYNRLREKTDEFLQEAKGKNIVGTYSIEEFVNALEKPRKILLMVKAGAPTDATIEQLKPHLEKGDIVIDGGNTYFKDTQRRNKELAELGIHFIGTGVSGGEEGALKGPSIMPGGQKEAHELVRPIFEAIAAKVDGEPCTTYIGPDGAGHYVKMVHNGIEYGDMQLIAEAYFLLKHVLGMDAAELHEVFADWNKGELNSYLIEITADIFTKIDEETGKPLVDVILDKAGQKGTGKWTSQNALDLGVPLPIITESVFARFLSAMKDERVKASKVLAGPAVKPFEGDRAHFIEAVRRALYMSKICSYAQGFAQMKAASEEYNWNLRYGDIAMIFRGGCIIRAQFLQKIKEAYDRDPALSNLLLDSYFKDIVERYQDALREIVATAAMRGIPVPGSASALAYYDSYRTAVLPANLIQAQRDYFGAHTYERVDKEGIFHTEWLK 469
                                    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       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461        


Chain B from PDB  Type:PROTEIN  Length:467
 aligned with I3NI58_GEOSE | I3NI58 from UniProtKB/TrEMBL  Length:470

    Alignment length:467
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       
         I3NI58_GEOSE     3 AKHQIGVIGLAVMGKNLALNIESKGYSVAVYNRLREKTDEFLQEAKGKNIVGTYSIEEFVNALEKPRKILLMVKAGAPTDATIEQLKPHLEKGDIVIDGGNTYFKDTQRRNKELAELGIHFIGTGVSGGEEGALKGPSIMPGGQKEAHELVRPIFEAIAAKVDGEPCTTYIGPDGAGHYVKMVHNGIEYGDMQLIAEAYFLLKHVLGMDAAELHEVFADWNKGELNSYLIEITADIFTKIDEETGKPLVDVILDKAGQKGTGKWTSQNALDLGVPLPIITESVFARFLSAMKDERVKASKVLAGPAVKPFEGDRAHFIEAVRRALYMSKICSYAQGFAQMKAASEEYNWNLRYGDIAMIFRGGCIIRAQFLQKIKEAYDRDPALSNLLLDSYFKDIVERYQDALREIVATAAMRGIPVPGSASALAYYDSYRTAVLPANLIQAQRDYFGAHTYERVDKEGIFHTEWL 469
               SCOP domains d2w8zb1 B:2-175 automated matches                                                                                                                                             d2w8zb2 B:176-468 automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2w8zB01 B:2-179 NAD(P)-binding Rossmann-like Domain                                                                                                                               2w8zB02 B:180-435 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                                                                                                                     2w8zB03 B:436-468                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh....eee..hhhhhhhh.....eeee....hhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhh...eeeeeeeehhhhhhhhh.eeeeeehhhhhhhhhhhhhhhh.ee..ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhhhhhh..........hhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w8z B   2 AKHQIGVIGLAVMGKNLALNIESKGYSVAVYNRLREKTDEFLQEAKGKNIVGTYSIEEFVNALEKPRKILLMVKAGAPTDATIEQLKPHLEKGDIVIDGGNTYFKDTQRRNKELAELGIHFIGTGVSGGEEGALKGPSIMPGGQKEAHELVRPIFEAIAAKVDGEPCTTYIGPDGAGHYVKMVHNGIEYGDMQLIAEAYFLLKHVLGMDAAELHEVFADWNKGELNSYLIEITADIFTKIDEETGKPLVDVILDKAGQKGTGKWTSQNALDLGVPLPIITESVFARFLSAMKDERVKASKVLAGPAVKPFEGDRAHFIEAVRRALYMSKICSYAQGFAQMKAASEEYNWNLRYGDIAMIFRGGCIIRAQFLQKIKEAYDRDPALSNLLLDSYFKDIVERYQDALREIVATAAMRGIPVPGSASALAYYDSYRTAVLPANLIQAQRDYFGAHTYERVDKEGIFHTEWL 468
                                    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       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461
   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 2W8Z)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (I3NI58_GEOSE | I3NI58)
molecular function
    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.
    GO:0004616    phosphogluconate dehydrogenase (decarboxylating) activity    Catalysis of the reaction: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH + H+.
biological process
    GO:0019521    D-gluconate metabolic process    The chemical reactions and pathways involving D-gluconate, the anion of D-gluconic acid, the aldonic acid derived from glucose.
    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.
    GO:0006098    pentose-phosphate shunt    The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.

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  2w8z
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  I3NI58_GEOSE | I3NI58
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  1.1.1.44
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 Related Entries

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

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(-) Related Entries Specified in the PDB File

2w90 GEOBACILLUS STEAROTHERMOPHILUS 6-PHOSPHOGLUCONATE WITH BOUND 6-PHOSPHOGLUCONATE