1S7C - JenaLib

Title :   CRYSTAL STRUCTURE OF MES BUFFER BOUND FORM OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI

Authors :   D. H. Shin, J. Thor, H. Yokota, R. Kim, S. H. Kim, Berkeley Structural G Center (Bsgc)

Date :   29 Jan 04 (Deposition) - 10 Aug 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.04

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Hypothetical, Structural Genomics, X-Ray Crytsallography, Oxidoreductase, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. H. Shin, J. Thor, H. Yokota, R. Kim, S. H. Kim
Crystal Structure Of Mes Buffer Bound Form Of Glyceraldehyd 3-Phosphate Dehydrogenase From Escherichia Coli
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_G3P1_ECOLI_001 *	Y	43	I	G3P1_ECOLI	---	---	A	Y	43	I
2	UniProt	VAR_G3P1_ECOLI_002 *	G	266	D	G3P1_ECOLI	---	---	A	G	266	D
3	UniProt	VAR_G3P1_ECOLI_003 *	E	267	A	G3P1_ECOLI	---	---	A	E	267	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_G3P1_ECOLI_001 *	Y	43	I	G3P1_ECOLI	---	---	A	Y	43	I
2	UniProt	VAR_G3P1_ECOLI_002 *	G	266	D	G3P1_ECOLI	---	---	A	G	266	D
3	UniProt	VAR_G3P1_ECOLI_003 *	E	267	A	G3P1_ECOLI	---	---	A	E	267	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (1, 1)

Exons (0, 0)

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 A from PDB  Type:PROTEIN  Length:330
 aligned with G3P1_ECOLI | P0A9B2 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:330
                                    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
           G3P1_ECOLI     2 TIKVGINGFGRIGRIVFRAAQKRSDIEIVAINDLLDADYMAYMLKYDSTHGRFDGTVEVKDGHLIVNGKKIRVTAERDPANLKWDEVGVDVVAEATGLFLTDETARKHITAGAKKVVMTGPSKDNTPMFVKGANFDKYAGQDIVSNASCTTNCLAPLAKVINDNFGIIEGLMTTVHATTATQKTVDGPSHKDWRGGRGASQNIIPSSTGAAKAVGKVLPELNGKLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAAAEGEMKGVLGYTEDDVVSTDFNGEVCTSVFDAKAGIALNDNFVKLVSWYDNETGYSNKVLDLIAHISK 331
               SCOP domains d1s7ca1 A:2-148,A:313-331 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                         d1s7ca2 A:149-312 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                  d1s7ca1             SCOP domains
               CATH domains 1s7cA01 A:2-148,A:315-331 NAD(P)-binding Rossmann-like Domain                                                                                      1s7cA02 A:149-314 Dihydrodipicolinate Reductase; domain 2                                                                                                             1s7cA01           CATH domains
               Pfam domains -Gp_dh_N-1s7cA02 A:3-150                                                                                                                             ----Gp_dh_C-1s7cA01 A:155-312                                                                                                                                     ------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhh....eeeeeee...hhhhhhhhhhh..........eee....eee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhhh...eeee...............hhhhh....eee..hhhhhhhhhhhhhhhhhhheeeeeeeeeee...............hhhhh......eeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee....eeee..eeeeeeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------I------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DA---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1s7c A   2 TIKVGINGFGRIGRIVFRAAQKRSDIEIVAINDLLDADYMAYMLKYDSTHGRFDGTVEVKDGHLIVNGKKIRVTAERDPANLKWDEVGVDVVAEATGLFLTDETARKHITAGAKKVVMTGPSKDNTPMFVKGANFDKYAGQDIVSNASCTTNCLAPLAKVINDNFGIIEGLMTTVHATTATQKTVDGPSHKDWRGGRGASQNIIPSSTGAAKAVGKVLPELNGKLTGMAFRVPTPNVSVVDLTVRLEKAATYEQIKAAVKAAAEGEMKGVLGYTEDDVVSTDFNGEVCTSVFDAKAGIALNDNFVKLVSWYDNETGYSNKVLDLIAHISK 331
                                    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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (2, 2)

Gene Ontology (12, 12)

Asymmetric Unit(hide GO term definitions)

Chain A (G3P1_ECOLI | P0A9B2)

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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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