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Title :   THE CRYSTAL STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM THE HYPERTHERMOPHILIC BACTERIUM THERMOTOGA MARITIMA AT 2.5 ANGSTROMS RESOLUTION

Authors :   I. Korndoerfer, B. Steipe, R. Huber, A. Tomschy, R. Jaenicke

Date :   17 Jan 95 (Deposition) - 31 Mar 95 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : O,Q
Biol. Unit 1: O,Q  (2x)

Keywords :   Oxidoreductase (Aldehy(D)-Nad(A)) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Korndorfer, B. Steipe, R. Huber, A. Tomschy, R. Jaenicke
The Crystal Structure Of Holo-Glyceraldehyde-3-Phosphate Dehydrogenase From The Hyperthermophilic Bacterium Thermotoga Maritima At 2. 5 A Resolution.
J. Mol. Biol. V. 246 511 1995
PubMed-ID: 7877172 | Reference-DOI: 10.1006/JMBI.1994.0103

Molecule 1 - HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
	Chains	:	O, Q
	EC Number	:	1.2.1.12
	Engineered	:	YES
	Expression System Vector Type	:	BACTERIUM
	Gene	:	TN10
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

		1	2
Asymmetric Unit	:	O	Q
Biological Unit 1 (2x)	:	O	Q

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
2	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR O:179 , ARG O:195 , ARG O:231 , NAD O:336 , HOH O:347 , HOH O:361	BINDING SITE FOR RESIDUE SO4 O 338
2	AC2	SOFTWARE	SER O:148 , CYS O:149 , THR O:150 , HIS O:176 , THR O:208 , GLY O:209 , HOH O:361 , HOH O:362 , HOH O:363 , HOH O:364	BINDING SITE FOR RESIDUE SO4 O 339
3	AC3	SOFTWARE	THR Q:179 , ASP Q:181 , ARG Q:195 , ARG Q:231 , NAD Q:336 , HOH Q:346 , HOH Q:353 , HOH Q:430	BINDING SITE FOR RESIDUE SO4 Q 338
4	AC4	SOFTWARE	SER Q:148 , CYS Q:149 , THR Q:150 , HIS Q:176 , THR Q:208 , GLY Q:209 , HOH Q:350 , HOH Q:353 , HOH Q:354 , HOH Q:430	BINDING SITE FOR RESIDUE SO4 Q 339
5	AC5	SOFTWARE	GLY O:7 , GLY O:9 , ARG O:10 , ILE O:11 , ASN O:31 , ASP O:32 , LEU O:33 , PRO O:77 , SER O:95 , THR O:96 , GLY O:97 , THR O:119 , ALA O:120 , ASN O:180 , ASN O:313 , TYR O:317 , SO4 O:338 , HOH O:345 , HOH O:346 , HOH O:347 , HOH O:348 , HOH O:351 , HOH O:366 , HOH O:369 , HOH O:422 , HOH O:423 , HOH O:424 , HOH O:426 , HOH Q:411	BINDING SITE FOR RESIDUE NAD O 336
6	AC6	SOFTWARE	GLY Q:7 , GLY Q:9 , ARG Q:10 , ILE Q:11 , ASN Q:31 , ASP Q:32 , LEU Q:33 , PRO Q:77 , SER Q:95 , THR Q:96 , GLY Q:97 , PHE Q:99 , THR Q:119 , ALA Q:120 , ASN Q:180 , ASN Q:313 , TYR Q:317 , SO4 Q:338 , HOH Q:341 , HOH Q:342 , HOH Q:343 , HOH Q:345 , HOH Q:346 , HOH Q:347 , HOH Q:348 , HOH Q:350 , HOH Q:351 , HOH Q:363 , HOH Q:366 , HOH Q:367	BINDING SITE FOR RESIDUE NAD Q 336

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

(no "Cis Peptide Bond" information available for 1HDG)

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GAPDH	PS00071	Glyceraldehyde 3-phosphate dehydrogenase active site.	G3P_THEMA	150-157	2	O:147-154 Q:147-154

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GAPDH	PS00071	Glyceraldehyde 3-phosphate dehydrogenase active site.	G3P_THEMA	150-157	4	O:147-154 Q:147-154

(no "Exon" information available for 1HDG)

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:332
 aligned with G3P_THEMA | P17721 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:332
                                    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  
           G3P_THEMA      2 ARVAINGFGRIGRLVYRIIYERKNPDIEVVAINDLTDTKTLAHLLKYDSVHKKFPGKVEYTENSLIVDGKEIKVFAEPDPSKLPWKDLGVDFVIESTGVFRNREKAELHLQAGAKKVIITAPAKGEDITVVIGCNEDQLKPEHTIISCASCTTNSIAPIVKVLHEKFGIVSGMLTTVHSYTNDQRVLDLPHKDLRRARAAAVNIIPTTTGAAKAVALVVPEVKGKLDGMAIRVPTPDGSITDLTVLVEKETTVEEVNAVMKEATEGRLKGIIGYNDEPIVSSDIIGTTFSGIFDATITNVIGGKLVKVASWYDNEYGYSNRVVDTLELLLKM  333
               SCOP domains d1hdgo1 O:1-148,O:313-331 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                            d1hdgo2 O:149-312 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                 d1hdgo1             SCOP domains
               CATH domains 1hdgO01 O:1-147,O:314-331 NAD(P)-binding Rossmann-like Domain                                                                                        1hdgO02 O:148-313 Dihydrodipicolinate Reductase; domain 2                                                                                                            1hdgO01            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhh.....eeeeee....hhhhhhhhh...........eee...eeee..eeeeee....hhh..hhhh...eeee.......hhhhhhhhh....eeee................hhh......eee...hhhhhhhhhhhhhhhhh.eeeeeeeeeee....................hhh..eee...hhhhhhhh.hhh...eeeeeeee.....eeeeeeeee.....hhhhhhhhhhhhh......eeee.....hhhh......eeee....eee...eeeeeeee...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1hdg O    1 ARVAINGFGRIGRLVYRIIYERKNPDIEVVAINDLTDTKTLAHLLKYDSVHKKFPGKVEYTENSLIVDGKEIKVFAEPDPSKLPWKDLGVDFVIESTGVFRNREKAELHLQAGAKKVIITAPAKGEDITVVIGCNEDQLKPEHTIISCASCTTNSIAPIVKVLHEKFGIVSGMLTTVHSYTNDQRVLDLPHKDLRRARAAAVNIIPTTTGAAKAVALVVPEVKGKLDGMAIRVPTPDGSITDLTVLVEKETTVEEVNAVMKEATEGRLKGIIGYNDEPIVSSDIIGTTFSGIFDATITNVIGGKLVKVASWYDNEYGYSNRVVDTLELLLKM  331
                                    10       18B        28     || 39        49        59        69        79        89        99       109       119   |   128       138       148       158       168       178       188|      199       209       219       229       239       249       259       269       279       289       299       309       319       329  
                                            18A|              34|                                                                                   122A                                                               188|                                                                                                                                             
                                             18B               36                                                                                                                                                       190

Chain Q from PDB  Type:PROTEIN  Length:332
 aligned with G3P_THEMA | P17721 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:332
                                    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  
           G3P_THEMA      2 ARVAINGFGRIGRLVYRIIYERKNPDIEVVAINDLTDTKTLAHLLKYDSVHKKFPGKVEYTENSLIVDGKEIKVFAEPDPSKLPWKDLGVDFVIESTGVFRNREKAELHLQAGAKKVIITAPAKGEDITVVIGCNEDQLKPEHTIISCASCTTNSIAPIVKVLHEKFGIVSGMLTTVHSYTNDQRVLDLPHKDLRRARAAAVNIIPTTTGAAKAVALVVPEVKGKLDGMAIRVPTPDGSITDLTVLVEKETTVEEVNAVMKEATEGRLKGIIGYNDEPIVSSDIIGTTFSGIFDATITNVIGGKLVKVASWYDNEYGYSNRVVDTLELLLKM  333
               SCOP domains d1hdgq1 Q:1-148,Q:313-331 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                            d1hdgq2 Q:149-312 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                 d1hdgq1             SCOP domains
               CATH domains 1hdgQ01 Q:1-147,Q:314-331 NAD(P)-binding Rossmann-like Domain                                                                                        1hdgQ02 Q:148-313 Dihydrodipicolinate Reductase; domain 2                                                                                                            1hdgQ01            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhh.....eeeeee....hhhhhhhhh...........eee...eeee..eeeeee....hhh..hhhh...eeee.......hhhhhhhhh....eeee.........................eee...hhhhhhhhhhhhhhhhh.eeeeeeeeeee.........................eee..hhhhhhhhh.hhh...eeeeeeee.....eeeeeeeee.....hhhhhhhhhhhhh......eeee.....hhh.......eeee....eee...eeeeeeee...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1hdg Q    1 ARVAINGFGRIGRLVYRIIYERKNPDIEVVAINDLTDTKTLAHLLKYDSVHKKFPGKVEYTENSLIVDGKEIKVFAEPDPSKLPWKDLGVDFVIESTGVFRNREKAELHLQAGAKKVIITAPAKGEDITVVIGCNEDQLKPEHTIISCASCTTNSIAPIVKVLHEKFGIVSGMLTTVHSYTNDQRVLDLPHKDLRRARAAAVNIIPTTTGAAKAVALVVPEVKGKLDGMAIRVPTPDGSITDLTVLVEKETTVEEVNAVMKEATEGRLKGIIGYNDEPIVSSDIIGTTFSGIFDATITNVIGGKLVKVASWYDNEYGYSNRVVDTLELLLKM  331
                                    10       18B        28     || 39        49        59        69        79        89        99       109       119   |   128       138       148       158       168       178       188|      199       209       219       229       239       249       259       269       279       289       299       309       319       329  
                                            18A|              34|                                                                                   122A                                                               188|                                                                                                                                             
                                             18B               36                                                                                                                                                       190

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 '\|'

Asymmetric 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)

Thermotoga maritima. Organism_taxid: 2336. (4)

1a	1hdgO02	O:148-313
1b	1hdgQ02	Q:148-313

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

Topology: Rossmann fold (7312)

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

Thermotoga maritima. Organism_taxid: 2336. (10)

2a	1hdgO01	O:1-147,O:314-331
2b	1hdgQ01	Q:1-147,Q:314-331

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

Asymmetric Unit(hide GO term definitions)

Chain O,Q (G3P_THEMA | P17721)

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.

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Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

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