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Title :   CRYSTAL STRUCTURE AND FUNCTIONAL ANALYSIS OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM ORYZA SATIVA

Authors :   Y. C. Tien, Y. H. Lin, S. L. Chang, C. J. Chen

Date :   15 Aug 08 (Deposition) - 18 Aug 09 (Release) - 18 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.77

Chains :   Asym./Biol. Unit : A,B,C,O

Keywords :   Gapdh, Glyceraldehyde-3-Phosphate, Oryza Sativa, Rice, Sulfate, Cytoplasm, Glycolysis, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. C. Tien, Y. H. Lin, S. L. Chang, C. J. Chen
Crystal Structure And Functional Analysis Of Glyceraldehyde-3-Phosphate Dehydrogenase From Oryza Sativa
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE, CYTOSOLIC
	Chains	:	O, A, B, C
	EC Number	:	1.2.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-SUMO
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	LIGAND BINDING
	Gene	:	GAPDH
	Organism Common	:	JAPANESE RICE
	Organism Scientific	:	ORYZA SATIVA JAPONICA GROUP
	Organism Taxid	:	39947
	Strain	:	JAPONICA CULTIVAR-GROUP
	Synonym	:	PP38

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	O

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 8)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR O:184 , THR O:186 , ARG O:236	BINDING SITE FOR RESIDUE SO4 O6920
2	AC2	SOFTWARE	SER O:153 , THR O:155 , THR O:156 , THR O:213 , GLY O:214 , ALA O:215	BINDING SITE FOR RESIDUE SO4 O6921
3	AC3	SOFTWARE	THR A:184 , THR A:186 , ARG A:236	BINDING SITE FOR RESIDUE SO4 A6922
4	AC4	SOFTWARE	SER A:153 , THR A:155 , THR A:213 , ALA A:215	BINDING SITE FOR RESIDUE SO4 A6923
5	AC5	SOFTWARE	SER B:153 , THR B:155 , THR B:213 , ALA B:215	BINDING SITE FOR RESIDUE SO4 B6924
6	AC6	SOFTWARE	THR B:184 , THR B:186 , ARG B:236	BINDING SITE FOR RESIDUE SO4 B6925
7	AC7	SOFTWARE	SER C:153 , THR C:155 , THR C:213 , GLY C:214 , ALA C:215	BINDING SITE FOR RESIDUE SO4 C6926
8	AC8	SOFTWARE	THR C:184 , THR C:186 , ARG C:236	BINDING SITE FOR RESIDUE SO4 C6927

(no "SS Bond" information available for 3E6A)

(no "Cis Peptide Bond" information available for 3E6A)

(no "SAP(SNP)/Variant" information available for 3E6A)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GAPDH	PS00071	Glyceraldehyde 3-phosphate dehydrogenase active site.	G3PC1_ORYSJ	152-159	4	A:152-159 B:152-159 C:152-159 O:152-159

(no "Exon" information available for 3E6A)

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
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Chain A from PDB  Type:PROTEIN  Length:334
 aligned with G3PC1_ORYSJ | Q0J8A4 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:334
                                    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    
          G3PC1_ORYSJ     3 KIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKT 336
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3e6aA01 A:3-152,A:319-336 NAD(P)-binding Rossmann-like Domain                                                                                         3e6aA02 A:153-318 Dihydrodipicolinate Reductase; domain 2                                                                                                             3e6aA01            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhh.............eee.....eee..ee.eee...hhhhhhhhhh...eeee........hhhhhh......eeee........................eee....hhhhhhhhhhhhhhhhheeeeeee.eee...............hhhhh......ee...hhhhhhhhhhhhhh.......eee.....eeeeeeeee....hhhhhhhhhhhhh.......eeee.....hhhhh.....eeee...........eeeeeee..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e6a A   3 KIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKT 336
                                    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

Chain B from PDB  Type:PROTEIN  Length:335
 aligned with G3PC1_ORYSJ | Q0J8A4 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:335
                                    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     
          G3PC1_ORYSJ     2 GKIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKT 336
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3e6aB01 B:2-152,B:319-336 NAD(P)-binding Rossmann-like Domain                                                                                          3e6aB02 B:153-318 Dihydrodipicolinate Reductase; domain 2                                                                                                             3e6aB01            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhh.....eeeeee....hhhhhhhhhhh....................hhhhh..eee...hhhhhhhhhhh..eeee......hhhhhhhhhhh....eee........................eee....hhhhhhhhhhhhhh........eeeee................hhhhhhhhhh.eeee.hhhhhhhhhh........eeeee......eeeeeeee.....hhhhhhhhhhhh.........eee....hhhhhh......eee....eeee..eeeeeeeehhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e6a B   2 GKIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKT 336
                                    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

Chain C from PDB  Type:PROTEIN  Length:335
 aligned with G3PC1_ORYSJ | Q0J8A4 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:335
                                    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     
          G3PC1_ORYSJ     2 GKIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKT 336
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3e6aC01 C:2-152,C:319-336 NAD(P)-binding Rossmann-like Domain                                                                                          3e6aC02 C:153-318 Dihydrodipicolinate Reductase; domain 2                                                                                                             3e6aC01            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh....................hhhhh..ee....hhhhhhhhhhh............hhhhhhhhhhhh...eee..............hhhhh.....eee....hhhhhhhhhhhhhhhhheeeeeeeee.................hhhhhhhhhh.eeee.hhhhhh.............eeee......eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee....eeee..eeeeeeeehhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e6a C   2 GKIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKT 336
                                    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

Chain O from PDB  Type:PROTEIN  Length:335
 aligned with G3PC1_ORYSJ | Q0J8A4 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:335
                                    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     
          G3PC1_ORYSJ     2 GKIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKT 336
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3e6aO01 O:2-152,O:319-336 NAD(P)-binding Rossmann-like Domain                                                                                          3e6aO02 O:153-318 Dihydrodipicolinate Reductase; domain 2                                                                                                             3e6aO01            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhh......eeeeeee....hhhhhhhhhhh...........................eee........hhhhhh..eeee...........hhhhhhh..eeee........................eee.......hhhhhhhhhhhhhheeeeeeeeee................................hhhhhhhhhh.........eeee......eeeeeeeee....hhhhhhhhhhhhhh......eeee....hhhhhh.....eeeeeeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e6a O   2 GKIKIGINGFGRIGRLVARVALQSEDVELVAVNDPFITTDYMTYMFKYDTVHGQWKHSDIKIKDSKTLLLGEKPVTVFGIRNPDEIPWAEAGAEYVVESTGVFTDKEKAAAHLKGGAKKVVISAPSKDAPMFVCGVNEDKYTSDIDIVSNASCTTNCLAPLAKVIHDNFGIIEGLMTTVHAITATQKTVDGPSSKDWRGGRAASFNIIPSSTGAAKAVGKVLPDLNGKLTGMSFRVPTVDVSVVDLTVRIEKAASYDAIKSAIKSASEGKLKGIIGYVEEDLVSTDFVGDSRSSIFDAKAGIALNDNFVKLVAWYDNEWGYSNRVIDLIRHMAKT 336
                                    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

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 '\|'

(no "SCOP Domain" information available for 3E6A)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Dihydrodipicolinate Reductase; domain 2 (182)

Homologous Superfamily: Dihydrodipicolinate Reductase; domain 2 (178)

Japanese rice (Oryza sativa japonica group) (1)

1a	3e6aA02	A:153-318
1b	3e6aB02	B:153-318
1c	3e6aC02	C:153-318
1d	3e6aO02	O:153-318

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Japanese rice (Oryza sativa japonica group) (1)

2a	3e6aB01	B:2-152,B:319-336
2b	3e6aC01	C:2-152,C:319-336
2c	3e6aO01	O:2-152,O:319-336
2d	3e6aA01	A:3-152,A:319-336

(no "Pfam Domain" information available for 3E6A)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,O (G3PC1_ORYSJ | Q0J8A4)

molecular function
	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: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:0006006	glucose metabolic process	The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
	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: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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3e6a)

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Description

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Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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