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(-) Description

Title :  GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
 
Authors :  M. N. Isupov, J. A. Littlechild
Date :  22 Jan 99  (Deposition) - 08 Oct 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  O,Q
Biol. Unit 1:  O,Q  (1x)
Biol. Unit 2:  O,Q  (2x)
Keywords :  Archaea; Hyperthermophile; Gapdh; Hyperthermophilic Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. N. Isupov, T. M. Fleming, A. R. Dalby, G. S. Crowhurst, P. C. Bourne, J. A. Littlechild
Crystal Structure Of The Glyceraldehyde-3-Phosphate Dehydrogenase From The Hyperthermophilic Archaeon Sulfolobu Solfataricus.
J. Mol. Biol. V. 291 651 1999
PubMed-ID: 10448043  |  Reference-DOI: 10.1006/JMBI.1999.3003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE)
    Cellular Location: CYTOPLASM
    Chains: O, Q
    EC Number: 1.2.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : OQ
Biological Unit 1 (1x): OQ
Biological Unit 2 (2x): OQ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1SO412Ligand/IonSULFATE ION
Biological Unit 2 (1, 24)
No.NameCountTypeFull Name
1SO424Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER O:138 , CYS O:139 , ASN O:140 , ARG O:166 , HIS O:192 , HIS O:193 , HOH O:617BINDING SITE FOR RESIDUE SO4 O 601
02AC2SOFTWARESER Q:138 , CYS Q:139 , ASN Q:140 , ARG Q:166 , HIS Q:192 , HIS Q:193 , HOH Q:667BINDING SITE FOR RESIDUE SO4 Q 602
03AC3SOFTWAREARG O:166 , ARG O:167 , HOH O:661 , HOH O:847BINDING SITE FOR RESIDUE SO4 O 603
04AC4SOFTWAREARG Q:166 , ARG Q:167BINDING SITE FOR RESIDUE SO4 Q 604
05AC5SOFTWARELYS O:33 , THR O:34 , SER O:35 , HOH O:777 , HOH O:894BINDING SITE FOR RESIDUE SO4 O 605
06AC6SOFTWARELYS Q:33 , THR Q:34 , SER Q:35 , HOH Q:744 , HOH Q:745BINDING SITE FOR RESIDUE SO4 Q 606
07AC7SOFTWAREPRO O:186 , SER O:191 , HIS O:192 , HOH O:636 , HOH O:728 , HOH O:784 , HOH O:799BINDING SITE FOR RESIDUE SO4 O 607
08AC8SOFTWAREPRO Q:186 , SER Q:191 , HIS Q:192 , HOH Q:736 , HOH Q:792BINDING SITE FOR RESIDUE SO4 Q 608
09AC9SOFTWARELYS O:131 , ARG Q:49 , PRO Q:66BINDING SITE FOR RESIDUE SO4 Q 609
10BC1SOFTWARETHR O:11 , LYS O:172 , GLU O:173 , HOH O:664 , HOH O:688BINDING SITE FOR RESIDUE SO4 O 610
11BC2SOFTWARELYS O:111 , ALA O:112 , LYS O:195 , HOH O:645 , HOH O:675 , HOH O:762 , HOH O:839BINDING SITE FOR RESIDUE SO4 O 611
12BC3SOFTWAREGLY Q:10 , THR Q:11 , LYS Q:172 , HOH Q:640BINDING SITE FOR RESIDUE SO4 Q 612
13CTOAUTHORCYS O:139 , HIS O:219CATALYTIC SITE IN SUBUNIT O
14CTQAUTHORCYS Q:139 , HIS Q:219CATALYTIC SITE IN SUBUNIT Q
15PIOAUTHORSER O:138 , ASN O:140 , ARG O:166 , HIS O:192 , HIS O:193INORGANIC PHOSPHATE BINDING SITE IN SUBUNIT Q
16PIQAUTHORSER Q:138 , ASN Q:140 , ARG Q:166 , HIS Q:192 , HIS Q:193INORGAINC PHOSPHATE BINDING SITE IN SUBUNIT Q
17PSOAUTHORARG O:166 , ARG O:167SUBSTRATE PHOSPHARE BINDING SITE IN SUBUNIT O
18PSQAUTHORARG Q:166 , ARG Q:167SUBSTRATE PHOSPHATE BINDING SITE IN SUBUNIT Q

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1O:123 -O:149
2Q:123 -Q:149

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly O:177 -Pro O:178
2Asp O:185 -Pro O:186
3Val O:189 -Pro O:190
4Gly Q:177 -Pro Q:178
5Asp Q:185 -Pro Q:186
6Val Q:189 -Pro Q:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B7G)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAPDHPS00071 Glyceraldehyde 3-phosphate dehydrogenase active site.G3P_SULSO137-144
 		  2O:137-144
Q:137-144
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAPDHPS00071 Glyceraldehyde 3-phosphate dehydrogenase active site.G3P_SULSO137-144
 		  2O:137-144
Q:137-144
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAPDHPS00071 Glyceraldehyde 3-phosphate dehydrogenase active site.G3P_SULSO137-144
 		  4O:137-144
Q:137-144

(-) Exons   (0, 0)

(no "Exon" information available for 1B7G)

(-) 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 O from PDB  Type:PROTEIN  Length:340
 aligned with G3P_SULSO | P39460 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:340
                                    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
            G3P_SULSO     1 MINVAVNGYGTIGKRVADAIIKQPDMKLVGVAKTSPNYEAFIAHRRGIRIYVPQQSIKKFEESGIPVAGTVEDLIKTSDIVVDTTPNGVGAQYKPIYLQLQRNAIFQGGEKAEVADISFSALCNYNEALGKKYIRVVSCNTTALLRTICTVNKVSKVEKVRATIVRRAADQKEVKKGPINSLVPDPATVPSHHAKDVNSVIRNLDIATMAVIAPTTLMHMHFINITLKDKVEKKDILSVLENTPRIVLISSKYDAEATAELVEVARDLKRDRNDIPEVMIFSDSIYVKDDEVMLMYAVHQESIVVPENIDAIRASMKLMSAEDSMRITNESLGILKGYLI 340
               SCOP domains d1b7go1 O:1-138,O:301-340 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                d1b7go2 O:139-300 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                d1b7go1 O:1-138,O:301-340                SCOP domains
               CATH domains 1b7gO01 O:1-136,O:308-327 NAD(P)-binding Rossmann-like Domain                                                                           1b7gO02 O:137-307,O:328-340 Dihydrodipicolinate Reductase; domain 2                                                                                                        1b7gO01             1b7gO02       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhh....eeeeeee.....hhhhhhhh........hhhhhhhhhh.......hhhhhhh..eeee.....hhhhhhhhhhh...eeee.....hhh..eee.hhhhhhhh....eeee..hhhhhhhhhhhhhhh...eeeeeeeeeee........................hhhhhhhh.....eeeeeeeee.....eeeeeeeee.....hhhhhhhhhh...eeee........hhhhhhhhhh...hhh....eeeehhh.eee..eeeeeeee....hhhhhhhhhhhhh.....hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------GAPDH   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b7g O   1 MVNVAVNGYGTIGKRVADAIIKQPDMKLVGVAKTSPNYEAFIAHRRGIRIYVPQQSIKKFEESGIPVAGTVEDLIKTSDIVVDTTPNGVGAQYKPIYLQLQRNAIFQGGEKAEVADISFSALCNYNEALGKKYIRVVSCNTTALLRTICTVNKVSKVEKVRATIVRRAADQKEVKKGPINSLVPDPATVPSHHAKDVNSVIRNLDIATMAVIAPTTLMHMHFINITLKDKVEKKDILSVLENTPRIVLISSKYDAEATAELVEVARDLKRDRNDIPEVMIFSDSIYVKDDEVMLMYAVHQESIVVPENIDAIRASMKLMSAEDSMRITNESLGILKGYLI 340
                                    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


Chain Q from PDB  Type:PROTEIN  Length:340
 aligned with G3P_SULSO | P39460 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:340
                                    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
            G3P_SULSO     1 MINVAVNGYGTIGKRVADAIIKQPDMKLVGVAKTSPNYEAFIAHRRGIRIYVPQQSIKKFEESGIPVAGTVEDLIKTSDIVVDTTPNGVGAQYKPIYLQLQRNAIFQGGEKAEVADISFSALCNYNEALGKKYIRVVSCNTTALLRTICTVNKVSKVEKVRATIVRRAADQKEVKKGPINSLVPDPATVPSHHAKDVNSVIRNLDIATMAVIAPTTLMHMHFINITLKDKVEKKDILSVLENTPRIVLISSKYDAEATAELVEVARDLKRDRNDIPEVMIFSDSIYVKDDEVMLMYAVHQESIVVPENIDAIRASMKLMSAEDSMRITNESLGILKGYLI 340
               SCOP domains d1b7gq1 Q:1-138,Q:301-340 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                d1b7gq2 Q:139-300 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                d1b7gq1 Q:1-138,Q:301-340                SCOP domains
               CATH domains 1b7gQ01 Q:1-136,Q:308-327 NAD(P)-binding Rossmann-like Domain                                                                           1b7gQ02 Q:137-307,Q:328-340 Dihydrodipicolinate Reductase; domain 2                                                                                                        1b7gQ01             1b7gQ02       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhh....eeeeeee.....hhhhhhhh........hhhhhhhhhh.......hhhhhh...eeee.....hhhhhhhhhhhh..eeee.....hhh..eee.hhhhhhhh....eeee..hhhhhhhhhhhhhhh...eeeeeeeeeee.........................hhhhhhh.....eeeeeeeee.....eeeeeeeee.....hhhhhhhh.....eeee........hhhhhhhhhh...hhh....eeeehhh.eee..eeeeeeee......hhhhhhhhhhh.....hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------GAPDH   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b7g Q   1 MVNVAVNGYGTIGKRVADAIIKQPDMKLVGVAKTSPNYEAFIAHRRGIRIYVPQQSIKKFEESGIPVAGTVEDLIKTSDIVVDTTPNGVGAQYKPIYLQLQRNAIFQGGEKAEVADISFSALCNYNEALGKKYIRVVSCNTTALLRTICTVNKVSKVEKVRATIVRRAADQKEVKKGPINSLVPDPATVPSHHAKDVNSVIRNLDIATMAVIAPTTLMHMHFINITLKDKVEKKDILSVLENTPRIVLISSKYDAEATAELVEVARDLKRDRNDIPEVMIFSDSIYVKDDEVMLMYAVHQESIVVPENIDAIRASMKLMSAEDSMRITNESLGILKGYLI 340
                                    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
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B7G)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain O,Q   (G3P_SULSO | P39460)
molecular function
    GO:0008839    4-hydroxy-tetrahydrodipicolinate reductase    Catalysis of the reaction: (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + H+.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    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:0043891    glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity    Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD(P)+ = 3-phospho-D-glyceroyl phosphate + NAD(P)H + H+.
    GO:0004365    glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity    Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH + H+.
    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:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
    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.
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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  1b7g
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