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(-) Description

Title :  X-RAY STRUCTURE OF 6-PHOSPHOGLUCONATE DEHYDROGENASE FROM THE PROTOZOAN PARASITE T. BRUCEI
 
Authors :  J. Dohnalek, C. Phillips, S. Gover, M. P. Barrett, M. J. Adams
Date :  16 Mar 98  (Deposition) - 11 Nov 98  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.82
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Choh(D)-Nadp+(B) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Phillips, J. Dohnalek, S. Gover, M. P. Barrett, M. J. Adams
A 2. 8 A Resolution Structure Of 6-Phosphogluconate Dehydrogenase From The Protozoan Parasite Trypanosoma Brucei: Comparison With The Sheep Enzyme Accounts For Differences In Activity With Coenzyme And Substrate Analogues.
J. Mol. Biol. V. 282 667 1998
PubMed-ID: 9737929  |  Reference-DOI: 10.1006/JMBI.1998.2059
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 6-PHOSPHOGLUCONATE DEHYDROGENASE
    Cell LineBL21
    ChainsA, B
    EC Number1.1.1.44
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System GeneT. BRUCEI GND
    Expression System PlasmidPT7GND
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneT. BRUCEI GND
    Organism ScientificTRYPANOSOMA BRUCEI
    Organism Taxid5691
    StrainBRUCEI
    Synonym6PGDH, 6-PGDH
    VariantTRUC427

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:193 , SER A:261 , LYS A:262 , ARG A:289 , HOH A:542 , ARG B:453 , HIS B:459BINDING SITE FOR RESIDUE SO4 A 505
2AC2SOFTWAREASN A:104 , LYS A:185 , ASN A:189 , HOH A:519 , HOH A:555BINDING SITE FOR RESIDUE SO4 A 507
3AC3SOFTWAREARG A:453 , HIS A:459 , TYR B:193 , SER B:261 , LYS B:262 , ARG B:289 , HOH B:554BINDING SITE FOR RESIDUE SO4 B 505
4AC4SOFTWAREASN B:104 , LYS B:185 , ASN B:189 , HOH B:521BINDING SITE FOR RESIDUE SO4 B 507

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:68 -Pro A:69
2Lys B:68 -Pro B:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
16PGDPS00461 6-phosphogluconate dehydrogenase signature.6PGD_TRYBB256-268
 
  2A:255-267
B:255-267

(-) Exons   (0, 0)

(no "Exon" information available for 1PGJ)

(-) 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:478
 aligned with 6PGD_TRYBB | P31072 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:478
                                    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       471        
           6PGD_TRYBB     2 SMDVGVVGLGVMGANLALNIAEKGFKVAVFNRTYSKSEEFMKANASAPFAGNLKAFETMEAFAASLKKPRKALILVQAGAATDSTTEQLKKVFEKGDILVDTGNAHFKDQGRRAQQLEAAGLRFLGMGISGGEEGARKGPAFFPGGTLSVWEEIRPIVEAAAAKADDGRPCVTMNGSGGAGSCVKMYHNSGEYAILQIWGEVFDILRAMGLNNDEVAAVLEDWKSKNFLKSYMLDISIAAARAKDKDGSYLTEHVMDRIGSKGTGLWSAQEALEIGVPAPSLNMAVVSRQFTMYKTERQANASNAPGITQSPGYTLKNKSPSGPEIKQLYDSVCIAIISCYAQMFQCLREMDKVHNFGLNLPATIATFRAGCILQGYLLKPMTEAFEKNPNISNLMCAFQTEIRAGLQNYRDMVALITSKLEVSIPVLSASLNYVTAMFTPTLKYGQLVSLQRDVFGRHGYERVDKDGRESFQWPELQ 479
               SCOP domains d1pgja2 A:1-178 6-phosphogluconate dehydrogenase                                                                                                                                  d1pgja1 A:179-478 6-phosphogluconate dehydrogenase (6PGD)                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1pgjA01 A:1-186 NAD(P)-binding Rossmann-like Domain                                                                                                                                       1pgjA02 A:187-444 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                                                                                                                       1pgjA03 A:445-478                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...hhhhhhhhhhhh....eeee...hhhhhhhhhh.........eee...hhhhhhh.....eeee.....hhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhh....eeeeeeee.hhhhhhh..eeeeee.hhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhh........hhhh.........hhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh............hhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh......hhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------6PGD         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pgj A   1 SMDVGVVGLGVMGANLALNIAEKGFKVAVFNRTYSKSEEFMKANASAPFAGNLKAFETMEAFAASLKKPRKALILVQAGAATDSTIEQLKKVFEKGDILVDTGNAHFKDQGRRAQQLEAAGLRFLGMGISGGEEGARKGPAFFPGGTLSVWEEIRPIVEAAAAKADDGRPCVTMNGSGGAGSCVKMYHNSGEYAILQIWGEVFDILRAMGLNNDEVAAVLEDWKSKNFLKSYMLDISIAAARAKDKDGSYLTEHVMDRIGSKGTGLWSAQEALEIGVPAPSLNMAVVSRQFTMYKTERQANASNAPGITQSPGYTLKNKSPSGPEIKQLYDSVCIAIISCYAQMFQCLREMDKVHNFGLNLPATIATFRAGCILQGYLLKPMTEAFEKNPNISNLMCAFQTEIRAGLQNYRDMVALITSKLEVSIPVLSASLNYVTAMFTPTLKYGQLVSLQRDVFGRHGYERVDKDGRESFQWPELQ 478
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470        

Chain B from PDB  Type:PROTEIN  Length:478
 aligned with 6PGD_TRYBB | P31072 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:478
                                    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       471        
           6PGD_TRYBB     2 SMDVGVVGLGVMGANLALNIAEKGFKVAVFNRTYSKSEEFMKANASAPFAGNLKAFETMEAFAASLKKPRKALILVQAGAATDSTTEQLKKVFEKGDILVDTGNAHFKDQGRRAQQLEAAGLRFLGMGISGGEEGARKGPAFFPGGTLSVWEEIRPIVEAAAAKADDGRPCVTMNGSGGAGSCVKMYHNSGEYAILQIWGEVFDILRAMGLNNDEVAAVLEDWKSKNFLKSYMLDISIAAARAKDKDGSYLTEHVMDRIGSKGTGLWSAQEALEIGVPAPSLNMAVVSRQFTMYKTERQANASNAPGITQSPGYTLKNKSPSGPEIKQLYDSVCIAIISCYAQMFQCLREMDKVHNFGLNLPATIATFRAGCILQGYLLKPMTEAFEKNPNISNLMCAFQTEIRAGLQNYRDMVALITSKLEVSIPVLSASLNYVTAMFTPTLKYGQLVSLQRDVFGRHGYERVDKDGRESFQWPELQ 479
               SCOP domains d1pgjb2 B:1-178 6-phosphogluconate dehydrogenase                                                                                                                                  d1pgjb1 B:179-478 6-phosphogluconate dehydrogenase (6PGD)                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1pgjB01 B:1-186 NAD(P)-binding Rossmann-like Domain                                                                                                                                       1pgjB02 B:187-444 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                                                                                                                       1pgjB03 B:445-478                  CATH domains
           Pfam domains (1) NAD_binding_2-1pgjB03 B:1-177                                                                                                                                                    ---6PGD-1pgjB01 B:181-475                                                                                                                                                                                                                                                                                 --- Pfam domains (1)
           Pfam domains (2) NAD_binding_2-1pgjB04 B:1-177                                                                                                                                                    ---6PGD-1pgjB02 B:181-475                                                                                                                                                                                                                                                                                 --- Pfam domains (2)
         Sec.struct. author ...eeee...hhhhhhhhhhhh....eeee...hhhhhhhhhh.........eee...hhhhhhh.....eeee.....hhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhh...eeeeeeee.hhhhhhh..eeeeee.hhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhh........hhhh.........hhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh............hhhhhhhhhh......hhhh.hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh......hhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------6PGD         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pgj B   1 SMDVGVVGLGVMGANLALNIAEKGFKVAVFNRTYSKSEEFMKANASAPFAGNLKAFETMEAFAASLKKPRKALILVQAGAATDSTIEQLKKVFEKGDILVDTGNAHFKDQGRRAQQLEAAGLRFLGMGISGGEEGARKGPAFFPGGTLSVWEEIRPIVEAAAAKADDGRPCVTMNGSGGAGSCVKMYHNSGEYAILQIWGEVFDILRAMGLNNDEVAAVLEDWKSKNFLKSYMLDISIAAARAKDKDGSYLTEHVMDRIGSKGTGLWSAQEALEIGVPAPSLNMAVVSRQFTMYKTERQANASNAPGITQSPGYTLKNKSPSGPEIKQLYDSVCIAIISCYAQMFQCLREMDKVHNFGLNLPATIATFRAGCILQGYLLKPMTEAFEKNPNISNLMCAFQTEIRAGLQNYRDMVALITSKLEVSIPVLSASLNYVTAMFTPTLKYGQLVSLQRDVFGRHGYERVDKDGRESFQWPELQ 478
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470        

   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

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: 6PGD_C (47)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (6PGD_TRYBB | P31072)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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