1SZJ - JenaLib

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Title :   STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE FROM PALINURUS VERSICOLOR REFINED 2.0 ANGSTROM RESOLUTION

Authors :   S. Song, J. Li, Z. Lin

Date :   04 Feb 97 (Deposition) - 16 Sep 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : G,R
Biol. Unit 1: G,R  (2x)

Keywords :   Oxidoreductase, D-Glyceraldehyde-3-Phosphate-Dehydrogenase, Molecular Symmetry, Allosterism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Y. Song, Y. G. Gao, J. M. Zhou, C. L. Tsou
Preliminary Crystallographic Studies Of Lobster D-Glyceraldehyde-3-Phosphate Dehydrogenase And The Modified Enzyme Carrying The Fluorescent Derivative.
J. Mol. Biol. V. 171 225 1983
PubMed-ID: 6655693 | Reference-DOI: 10.1016/S0022-2836(83)80355-6
(for further references see the PDB file header)

Molecule 1 - D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE
	Chains	:	G, R
	EC Number	:	1.2.1.12
	Fragment	:	NAD+ BINDING DOMAIN AND CATALYTIC DOMAIN
	Organ	:	TAIL
	Organism Common	:	SOUTH CHINA SEA LOBSTER
	Organism Scientific	:	PALINURUS VERSICOLOR
	Organism Taxid	:	82835
	Other Details	:	COMPLEX WITH NAD+
	Tissue	:	TAIL MUSCLE

		1	2
Asymmetric Unit	:	G	R
Biological Unit 1 (2x)	:	G	R

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 (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER G:148 , THR G:208 , GLY G:209 , ALA G:210 , HOH G:541 , HOH G:600 , HOH G:671	BINDING SITE FOR RESIDUE SO4 G 501
2	AC2	SOFTWARE	THR G:179 , THR G:181 , ARG G:231 , NAD G:335 , HOH G:546	BINDING SITE FOR RESIDUE SO4 G 502
3	AC3	SOFTWARE	SER R:148 , THR R:208 , GLY R:209 , ALA R:210 , HOH R:616	BINDING SITE FOR RESIDUE SO4 R 501
4	AC4	SOFTWARE	THR R:179 , THR R:181 , ARG R:231 , NAD R:335	BINDING SITE FOR RESIDUE SO4 R 502
5	AC5	SOFTWARE	ASN G:6 , GLY G:7 , PHE G:8 , GLY G:9 , ARG G:10 , ILE G:11 , ASN G:31 , ASP G:32 , PRO G:33 , PHE G:34 , MET G:77 , SER G:95 , THR G:96 , GLY G:97 , SER G:119 , ALA G:120 , CYS G:149 , ALA G:180 , ASN G:313 , TYR G:317 , SO4 G:502 , HOH G:505 , HOH G:513 , HOH G:514 , HOH G:522 , HOH G:577 , HOH G:601 , HOH G:619 , HOH G:636 , HOH G:688	BINDING SITE FOR RESIDUE NAD G 335
6	AC6	SOFTWARE	ASN R:6 , GLY R:7 , GLY R:9 , ARG R:10 , ILE R:11 , ASN R:31 , ASP R:32 , PRO R:33 , PHE R:34 , MET R:77 , SER R:95 , THR R:96 , GLY R:97 , SER R:119 , ALA R:120 , CYS R:149 , ASN R:313 , SO4 R:502 , HOH R:507 , HOH R:508 , HOH R:522 , HOH R:595 , HOH R:596 , HOH R:597	BINDING SITE FOR RESIDUE NAD R 335
7	ACT	UNKNOWN	CYS G:149 , HIS G:176	ACTIVE SITE RESIDUES CYS 149 AND HIS 176

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

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

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

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_PANVR	146-153	2	G:147-154 R: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_PANVR	146-153	4	G:147-154 R:147-154

(no "Exon" information available for 1SZJ)

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 G from PDB  Type:PROTEIN  Length:333
 aligned with G3P_PANVR | P56649 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:333
                                    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   
            G3P_PANVR     1 SKIGINGFGRIGRLVLRAALEMGAQVVAVNDPFIALEYMVYMFKYDSTHGMFKGEVKAEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTTIEKASAHFKGGAKKVIISAPSADAPMFVCGVNLEKYSKDMKVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQNIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPNVSVVDLTVRLGKECSYDDIKAAMKAASEGPLQGVLGYTEDDVVSCDFTGDNRSSIFDAKAGIQLSKTFVKVVSWYDNEFGYSQRVIDLIKHMQKVDSA 333
               SCOP domains d1szjg1 G:1-148,G:313-334 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                         d1szjg2 G:149-312 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                  d1szjg1                SCOP domains
               CATH domains 1szjG01 G:1-147,G:314-333 NAD(P)-binding Rossmann-like Domain                                                                                     1szjG02 G:148-313 Dihydrodipicolinate Reductase; domain 2                                                                                                             1szjG01             - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhh....eeeee.....hhhhhhhhh...........eeee..eeee..eeeeee....hhh..hhhh...eeee.......hhhhhhhhhh...eeee...............hhh......eee...hhhhhhhhhhhhhhhhh.eeeeeeeeee.................hhh.......eeee..hhhhhhhh.hhh...eeeeeee......eeeeeeeee.....hhhhhhhhhhhhh......eeee.....hhhh......eeee....eeee..eeeeeeee...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1szj G   1 SKIGINGFGRIGRLVLRAALEMGAQVVAVNDPFIALEYMVYMFKYDSTHGMFKGEVKAEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTTIEKASAHFKGGAKKVIISAPSADAPMFVCGVNLEKYSKDMKVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQNIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPNVSVVDLTVRLGKECSYDDIKAAMKAASEGPLQGVLGYTEDDVVSCDFTGDNRSSIFDAKAGIQLSKTFVKVVSWYDNEFGYSQRVIDLIKHMQKVDSA 334
                                    10        20  ||    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   
                                                 23|                                                                                                                                                                                                                                                                                                                     
                                                  25

Chain R from PDB  Type:PROTEIN  Length:333
 aligned with G3P_PANVR | P56649 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:333
                                    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   
            G3P_PANVR     1 SKIGINGFGRIGRLVLRAALEMGAQVVAVNDPFIALEYMVYMFKYDSTHGMFKGEVKAEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTTIEKASAHFKGGAKKVIISAPSADAPMFVCGVNLEKYSKDMKVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQNIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPNVSVVDLTVRLGKECSYDDIKAAMKAASEGPLQGVLGYTEDDVVSCDFTGDNRSSIFDAKAGIQLSKTFVKVVSWYDNEFGYSQRVIDLIKHMQKVDSA 333
               SCOP domains d1szjr1 R:1-148,R:313-334 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                         d1szjr2 R:149-312 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                  d1szjr1                SCOP domains
               CATH domains 1szjR01 R:1-147,R:314-333 NAD(P)-binding Rossmann-like Domain                                                                                     1szjR02 R:148-313 Dihydrodipicolinate Reductase; domain 2                                                                                                             1szjR01             - CATH domains
           Pfam domains (1) Gp_dh_N-1szjR03 R:1-149                                                                                                                             ----Gp_dh_C-1szjR01 R:154-311                                                                                                                                     ----------------------- Pfam domains (1)
           Pfam domains (2) Gp_dh_N-1szjR04 R:1-149                                                                                                                             ----Gp_dh_C-1szjR02 R:154-311                                                                                                                                     ----------------------- Pfam domains (2)
         Sec.struct. author ..eeee...hhhhhhhhhhhh....eeeee.....hhhhhhhhh...........eeee..eeee..eeeeee....hhh..hhhh...eeee.......hhhhhhhh.....eeee...............hhh......eee...hhhhhhhhhhhhhhhhh.eeeeeeeeee.................hhh.......eee...hhhhhhhh.hhh...eeeeeee......eeeeeeeee.....hhhhhhhhhhhhh......eeee.....hhhh......eeeehhh.eeee..eeeeeeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1szj R   1 SKIGINGFGRIGRLVLRAALEMGAQVVAVNDPFIALEYMVYMFKYDSTHGMFKGEVKAEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTTIEKASAHFKGGAKKVIISAPSADAPMFVCGVNLEKYSKDMKVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQNIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPNVSVVDLTVRLGKECSYDDIKAAMKAASEGPLQGVLGYTEDDVVSCDFTGDNRSSIFDAKAGIQLSKTFVKVVSWYDNEFGYSQRVIDLIKHMQKVDSA 334
                                    10        20  ||    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   
                                                 23|                                                                                                                                                                                                                                                                                                                     
                                                  25

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)

South china sea lobster (Palinurus versicolor) (5)

1a	1szjG02	G:148-313
1b	1szjR02	R:148-313

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

Topology: Rossmann fold (7312)

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

South china sea lobster (Palinurus versicolor) (5)

2a	1szjG01	G:1-147,G:314-333
2b	1szjR01	R:1-147,R:314-333

Asymmetric Unit(hide GO term definitions)

Chain G,R (G3P_PANVR | P56649)

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 Unit
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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