2P4Q - JenaLib

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Title :   CRYSTAL STRUCTURE ANALYSIS OF GND1 IN SACCHAROMYCES CEREVISIAE

Authors :   W. He, Y. Wang, W. Liu, C. Z. Zhou

Date :   12 Mar 07 (Deposition) - 24 Jul 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.37

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. He, Y. Wang, W. Liu, C. Z. Zhou
Crystal Structure Of Saccharomyces Cerevisiae 6-Phosphogluconate Dehydrogenase Gnd1
Bmc Struct. Biol. V. 7 38 2007
PubMed-ID: 17570834 | Reference-DOI: 10.1186/1472-6807-7-38

Molecule 1 - 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING 1
	Chains	:	A
	EC Number	:	1.1.1.44
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	ROSSETTA(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GND1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Strain	:	S288C

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	FLC	2	Ligand/Ion	CITRATE ANION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	FLC	4	Ligand/Ion	CITRATE ANION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:189 , TYR A:190 , MET A:193 , GLN A:258 , LYS A:259 , THR A:261 , ARG A:286 , ARG A:446 , HIS A:452 , FLC A:502	BINDING SITE FOR RESIDUE FLC A 501
2	AC2	SOFTWARE	ASN A:102 , SER A:128 , GLY A:130 , LYS A:182 , HIS A:185 , ASN A:186 , GLU A:189 , ILE A:366 , HIS A:452 , FLC A:501	BINDING SITE FOR RESIDUE FLC A 502

(no "SS Bond" information available for 2P4Q)

Asymmetric Unit

No.	Residues
1	Arg A:66	-	Pro A:67

(no "SAP(SNP)/Variant" information available for 2P4Q)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	6PGD	PS00461	6-phosphogluconate dehydrogenase signature.	6PGD1_YEAST	252-264	1	A:252-264

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	6PGD	PS00461	6-phosphogluconate dehydrogenase signature.	6PGD1_YEAST	252-264	2	A:252-264

Asymmetric Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YHR183W	1	YHR183W.1	VIII:470960-472429	1470	6PGD1_YEAST	1-489	489	1	A:1-476	476

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:476
 aligned with 6PGD1_YEAST | P38720 from UniProtKB/Swiss-Prot  Length:489

    Alignment length:476
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470      
          6PGD1_YEAST     1 MSADFGLIGLAVMGQNLILNAADHGFTVCAYNRTQSKVDHFLANEAKGKSIIGATSIEDFISKLKRPRKVMLLVKAGAPVDALINQIVPLLEKGDIIIDGGNSHFPDSNRRYEELKKKGILFVGSGVSGGEEGARYGPSLMPGGSEEAWPHIKNIFQSISAKSDGEPCCEWVGPAGAGHYVKMVHNGIEYGDMQLICEAYDIMKRLGGFTDKEISDVFAKWNNGVLDSFLVEITRDILKFDDVDGKPLVEKIMDTAGQKGTGKWTAINALDLGMPVTLIGEAVFARCLSALKNERIRASKVLPGPEVPKDAVKDREQFVDDLEQALYASKIISYAQGFMLIREAAATYGWKLNNPAIALMWRGGCIIRSVFLGQITKAYREEPDLENLLFNKFFADAVTKAQSGWRKSIALATTYGIPTPAFSTALSFYDGYRSERLPANLLQAQRDYFGAHTFRVLPECASDNLPVDKDIHINWT 476
               SCOP domains d2p4qa1 A:1-175 automated matches                                                                                                                                              d2p4qa2 A:176-476 automated matches                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2p4qA01 A:1-179 NAD(P)-binding Rossmann-like Domain                                                                                                                                2p4qA02 A:180-435 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                                                                                                                     ----------------------------------------- CATH domains
               Pfam domains -NAD_binding_2-2p4qA02 A:2-174                                                                                                                                                ---6PGD-2p4qA01 A:178-476                                                                                                                                                                                                                                                                                      Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhh...eeee...hhhhhhhhhh......ee...hhhhhhhh.....eeee....hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhh.eeeeee...hhhhhhhhhhhhh.ee..ee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhh.......hhhhhh.......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------6PGD         -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-476 UniProt: 1-489 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                           Transcript 1
                 2p4q A   1 MSADFGLIGLAVMGQNLILNAADHGFTVCAYNRTQSKVDHFLANEAKGKSIIGATSIEDFISKLKRPRKVMLLVKAGAPVDALINQIVPLLEKGDIIIDGGNSHFPDSNRRYEELKKKGILFVGSGVSGGEEGARYGPSLMPGGSEEAWPHIKNIFQSISAKSDGEPCCEWVGPAGAGHYVKMVHNGIEYGDMQLICEAYDIMKRLGGFTDKEISDVFAKWNNGVLDSFLVEITRDILKFDDVDGKPLVEKIMDTAGQKGTGKWTAINALDLGMPVTLIGEAVFARCLSALKNERIRASKVLPGPEVPKDAVKDREQFVDDLEQALYASKIISYAQGFMLIREAAATYGWKLNNPAIALMWRGGCIIRSVFLGQITKAYREEPDLENLLFNKFFADAVTKAQSGWRKSIALATTYGIPTPAFSTALSFYDGYRSERLPANLLQAQRDYFGAHTFRVLPECASDNLPVDKDIHINWT 476
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470

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(hide GO term definitions)

Chain A (6PGD1_YEAST | P38720)

molecular function
	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:0004616	phosphogluconate dehydrogenase (decarboxylating) activity	Catalysis of the reaction: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH + H+.
biological process
	GO:0019521	D-gluconate metabolic process	The chemical reactions and pathways involving D-gluconate, the anion of D-gluconic acid, the aldonic acid derived from glucose.
	GO:0034599	cellular response to oxidative stress	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	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.
	GO:0006098	pentose-phosphate shunt	The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
	GO:0009051	pentose-phosphate shunt, oxidative branch	The branch of the pentose-phosphate shunt which involves the oxidation of glucose 6-P and produces ribulose 5-P, reduced NADP+ and carbon dioxide (CO2).
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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		Arg A:66 - Pro A:67	[ RasMol ]

Biological Unit
	Complete Structure
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Description

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