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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
 
Authors :  A. D. Malay, Y. Bessho, B. Padmanabhan, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  02 May 07  (Deposition) - 06 Nov 07  (Release) - 09 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glyceraldehyde 3-Phosphate Binding, Alpha And Beta Proteins (A/B) Class, Mj1146, 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 :  A. D. Malay, Y. Bessho, M. J. Ellis, S. V. Antonyuk, R. W. Strange, S. S. Hasnain, A. Shinkai, B. Padmanabhan, S. Yokoyama
Structure Of Glyceraldehyde-3-Phosphate Dehydrogenase From The Archaeal Hyperthermophile Methanocaldococcus Jannaschii.
Acta Crystallogr. , Sect. F V. 65 1227 2009
PubMed-ID: 20054117  |  Reference-DOI: 10.1107/S1744309109047046

(-) Compounds

Molecule 1 - GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.2.1.59
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 243232
    Strain: DSM2661
    Synonym: GAPDH, NAD(P)-DEPENDENT GLYCERALDEHYDE-3- PHOSPHATE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:8 , GLY B:9 , TYR B:10 , GLY B:11 , SER B:12 , ILE B:13 , LYS B:34 , THR B:35 , LYS B:36 , ALA B:54 , GLY B:88 , ALA B:89 , PRO B:90 , ILE B:93 , ASN B:97 , GLN B:112 , GLY B:114 , CYS B:144 , ARG B:172 , ASP B:175 , GLN B:307 , HOH B:1004 , HOH B:1005 , HOH B:1062 , HOH B:1075 , HOH B:1119 , HOH B:1127 , HOH B:1142BINDING SITE FOR RESIDUE NAP B 1001
2AC2SOFTWAREASN A:8 , GLY A:9 , TYR A:10 , GLY A:11 , SER A:12 , ILE A:13 , LYS A:34 , THR A:35 , LYS A:36 , ALA A:54 , GLY A:88 , ALA A:89 , PRO A:90 , ILE A:93 , ASN A:97 , GLN A:112 , GLY A:114 , CYS A:144 , ARG A:172 , ASP A:175 , GLN A:307 , HOH A:2025 , HOH A:2038 , HOH A:2045 , HOH A:2099 , HOH A:2100 , HOH A:2105 , HOH A:2112BINDING SITE FOR RESIDUE NAP A 2001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gly A:182 -Pro A:183
2Asn A:190 -Pro A:191
3Val A:194 -Pro A:195
4Gly B:182 -Pro B:183
5Asn B:190 -Pro B:191
6Val B:194 -Pro B:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAPDHPS00071 Glyceraldehyde 3-phosphate dehydrogenase active site.G3P_METJA142-149
 		  2A:142-149
B:142-149

(-) Exons   (0, 0)

(no "Exon" information available for 2YYY)

(-) 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:342
 aligned with G3P_METJA | Q58546 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:342
                                    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  
            G3P_METJA     2 PAKVLINGYGSIGKRVADAVSMQDDMEVIGVTKTKPDFEARLAVEKGYKLFVAIPDNERVKLFEDAGIPVEGTILDIIEDADIVVDGAPKKIGKQNLENIYKPHKVKAILQGGEKAKDVEDNFNALWSYNRCYGKDYVRVVSCNTTGLCRILYAINSIADIKKARIVLVRRAADPNDDKTGPVNAITPNPVTVPSHHGPDVVSVVPEFEGKILTSAVIVPTTLMHMHTLMVEVDGDVSRDDILEAIKKTPRIITVRAEDGFSSTAKIIEYGRDLGRLRYDINELVVWEESINVLENEIFLMQAVHQESIVIPENIDCIRAMLQMEEDNFKSIEKTNKAMGIQ 343
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2yyyA01 A:2-142,A:311-343 NAD(P)-binding Rossmann-like Domain                                                                                2yyyA02 A:143-310 Dihydrodipicolinate Reductase; domain 2                                                                                                               2yyyA01 A:2-142,A:311-343         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhh...eee...hhhhhhhhhhh......hhhhhhhhh.eeee....hhhhhhhhhh......eeee....hhhhh.eee....hhhhhh...eeee.hhhhhhhhhhhhhhhh..eeeeeeeeeeee...............ee.......hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeee...hhhhhhhhhhhh..eeeehhhhh..hhhhhhhhhhhhhhhhhh...eeee.hhheee..eeeeeeee.....hhhhhhhhhhhhh....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------GAPDH   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yyy A   2 PAKVLINGYGSIGKRVADAVSMQDDMEVIGVTKTKPDFEARLAVEKGYKLFVAIPDNERVKLFEDAGIPVEGTILDIIEDADIVVDGAPKKIGKQNLENIYKPHKVKAILQGGEKAKDVEDNFNALWSYNRCYGKDYVRVVSCNTTGLCRILYAINSIADIKKARIVLVRRAADPNDDKTGPVNAITPNPVTVPSHHGPDVVSVVPEFEGKILTSAVIVPTTLMHMHTLMVEVDGDVSRDDILEAIKKTPRIITVRAEDGFSSTAKIIEYGRDLGRLRYDINELVVWEESINVLENEIFLMQAVHQESIVIPENIDCIRAMLQMEEDNFKSIEKTNKAMGIQ 343
                                    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  


Chain B from PDB  Type:PROTEIN  Length:342
 aligned with G3P_METJA | Q58546 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:342
                                    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  
            G3P_METJA     2 PAKVLINGYGSIGKRVADAVSMQDDMEVIGVTKTKPDFEARLAVEKGYKLFVAIPDNERVKLFEDAGIPVEGTILDIIEDADIVVDGAPKKIGKQNLENIYKPHKVKAILQGGEKAKDVEDNFNALWSYNRCYGKDYVRVVSCNTTGLCRILYAINSIADIKKARIVLVRRAADPNDDKTGPVNAITPNPVTVPSHHGPDVVSVVPEFEGKILTSAVIVPTTLMHMHTLMVEVDGDVSRDDILEAIKKTPRIITVRAEDGFSSTAKIIEYGRDLGRLRYDINELVVWEESINVLENEIFLMQAVHQESIVIPENIDCIRAMLQMEEDNFKSIEKTNKAMGIQ 343
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2yyyB01 B:2-142,B:311-343 NAD(P)-binding Rossmann-like Domain                                                                                2yyyB02 B:143-310 Dihydrodipicolinate Reductase; domain 2                                                                                                               2yyyB01 B:2-142,B:311-343         CATH domains
           Pfam domains (1) -Gp_dh_N-2yyyB03 B:3-144                                                                                                                       ----Gp_dh_C-2yyyB01 B:149-305                                                                                                                                    -------------------------------------- Pfam domains (1)
           Pfam domains (2) -Gp_dh_N-2yyyB04 B:3-144                                                                                                                       ----Gp_dh_C-2yyyB02 B:149-305                                                                                                                                    -------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhh...eee...hhhhhhhhhhhh.....hhhhhhhhh.eeee....hhhhhhhhhh......eeee....hhhhh.eee.............eeee.hhhhhhhhhhhhhhhh..eeeeeeeeeeee...............ee.......hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeee...hhhhhhhhhhhh..eeeehhhhh..hhhhhhhhhhhhhhhhhh...eeee.hhheee..eeeeeeee.....hhhhhhhhhhhhh....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------GAPDH   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yyy B   2 PAKVLINGYGSIGKRVADAVSMQDDMEVIGVTKTKPDFEARLAVEKGYKLFVAIPDNERVKLFEDAGIPVEGTILDIIEDADIVVDGAPKKIGKQNLENIYKPHKVKAILQGGEKAKDVEDNFNALWSYNRCYGKDYVRVVSCNTTGLCRILYAINSIADIKKARIVLVRRAADPNDDKTGPVNAITPNPVTVPSHHGPDVVSVVPEFEGKILTSAVIVPTTLMHMHTLMVEVDGDVSRDDILEAIKKTPRIITVRAEDGFSSTAKIIEYGRDLGRLRYDINELVVWEESINVLENEIFLMQAVHQESIVIPENIDCIRAMLQMEEDNFKSIEKTNKAMGIQ 343
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 2YYY)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: GADPH_aa-bio_dh (59)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (G3P_METJA | Q58546)
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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