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Title :   CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM

Authors :   M. J. Adams, C. Phillips, S. Gover, C. E. Naylor

Date :   18 Jul 94 (Deposition) - 27 Feb 95 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Oxidoreductase (Choh(D)-Nadp+(A)) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Adams, G. H. Ellis, S. Gover, C. E. Naylor, C. Phillips
Crystallographic Study Of Coenzyme, Coenzyme Analogue And Substrate Binding In 6-Phosphogluconate Dehydrogenase: Implications For Nadp Specificity And The Enzyme Mechanism.
Structure V. 2 651 1994
PubMed-ID: 7922042 | Reference-DOI: 10.1016/S0969-2126(00)00066-6
(for further references see the PDB file header)

Molecule 1 - 6-PHOSPHOGLUCONATE DEHYDROGENASE
	Chains	:	A
	EC Number	:	1.1.1.44
	Engineered	:	YES
	Organism Common	:	SHEEP
	Organism Scientific	:	OVIS ARIES
	Organism Taxid	:	9940

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	6PG	1	Ligand/Ion	6-PHOSPHOGLUCONIC ACID
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	6PG	2	Ligand/Ion	6-PHOSPHOGLUCONIC ACID
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:102 , SER A:128 , GLY A:129 , LYS A:183 , ASN A:187 , GLU A:190 , TYR A:191 , LYS A:260 , THR A:262 , ARG A:287 , ILE A:366 , ARG A:446 , HIS A:452 , HOH A:528 , HOH A:1109 , HOH A:1232	BINDING SITE FOR RESIDUE 6PG A 502
2	AC2	SOFTWARE	LYS A:50 , GLY A:211 , HIS A:212 , HIS A:248 , HOH A:636 , HOH A:1164	BINDING SITE FOR RESIDUE SO4 A 508

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

Asymmetric Unit

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	6PGD	PS00461	6-phosphogluconate dehydrogenase signature.	6PGD_SHEEP	254-266	1	A:253-265

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	6PGD	PS00461	6-phosphogluconate dehydrogenase signature.	6PGD_SHEEP	254-266	2	A:253-265

(no "Exon" information available for 1PGP)

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:473
 aligned with 6PGD_SHEEP | P00349 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:473
                                    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       341       351       361       371       381       391       401       411       421       431       441       451       461       471   
           6PGD_SHEEP     2 AQADIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVDDFLANEAKGTKVLGAHSLEEMVSKLKKPRRIILLVKAGQAVDNFIEKLVPLLDIGDIIIDGGNSEYRDTMRRCRDLKDKGILFVGSGVSGGEDGARYGPSLMPGGNKEAWPHIKAIFQGIAAKVGTGEPCCDWVGDDGAGHFVKMVHNGIEYGDMQLICEAYHLMKDVLGLGHKEMAKAFEEWNKTELDSFLIEITASILKFQDADGKHLLPKIRDSAGQKGTGKWTAISALEYGVPVTLIGEAVFARCLSSLKDERIQASKKLKGPQNIPFEGDKKSFLEDIRKALYASKIISYAQGFMLLRQAATEFGWTLNYGGIALMWRGGCIIRSVFLGKIKDAFDRNPGLQNLLLDDFFKSAVENCQDSWRRAISTGVQAGIPMPCFTTALSFYDGYRHAMLPANLIQAQRDYFGAHTYELLAKPGQFIHTNWTGHGG 474
               SCOP domains d1pgpa2 A:1-176 6-phosphogluconate dehydrogenase                                                                                                                                d1pgpa1 A:177-473 6-phosphogluconate dehydrogenase (6PGD)                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1pgpA01 A:1-180 NAD(P)-binding Rossmann-like Domain                                                                                                                                 1pgpA02 A:181-435 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                                                                                                                    1pgpA03 A:436-473                      CATH domains
               Pfam domains -NAD_binding_2-1pgpA02 A:2-175                                                                                                                                                 ---6PGD-1pgpA01 A:179-469                                                                                                                                                                                                                                                                             ---- Pfam domains
         Sec.struct. author ....eeee...hhhhhhhhhhhh....eeee....hhhhhhhh........ee...hhhhhhh.....eeee.....hhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhh...eeeeeeee.hhhhhhh..eeeeee....hhhhhhhhhhh..............ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.......hhhhhhhhhhh.....................hhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh..........hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------6PGD         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pgp A   1 AQADIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVDDFLANEAKGTKVLGAHSLEEMVSKLKKPRRIILLVKAGQAVDNFIEKLVPLLDIGDIIIDGGNSEYRDTMRRCRDLKDKGILFVGSGVSGGEDGARYGPSLMPGGNKEAWPHIKAIFQGIAAKVGTGEPCCDWVGDDGAGHFVKMVHNGIEYGDMQLICEAYHLMKDVLGLGHKEMAKAFEEWNKTELDSFLIEITASILKFQDADGKHLLPKIRDSAGQKGTGKWTAISALEYGVPVTLIGEAVFARCLSSLKDERIQASKKLKGPQNIPFEGDKKSFLEDIRKALYASKIISYAQGFMLLRQAATEFGWTLNYGGIALMWRGGCIIRSVFLGKIKDAFDRNPGLQNLLLDDFFKSAVENCQDSWRRAISTGVQAGIPMPCFTTALSFYDGYRHAMLPANLIQAQRDYFGAHTYELLAKPGQFIHTNWTGHGG 473
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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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: 6PGD_C (47)

Family: 6PGD (10)

Ovis aries (Sheep) (5)

6PGD-1pgpA01

A:179-469

Clan: NADP_Rossmann (1239)

Family: NAD_binding_2 (15)

Ovis aries (Sheep) (5)

NAD_binding_2-1pgpA02

A:2-175

Asymmetric Unit(hide GO term definitions)

Chain A (6PGD_SHEEP | P00349)

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: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.
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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		Lys A:66 - Pro A:67	[ RasMol ]

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	6PGD_SHEEP \| P00349	:	1pgn 1pgo 1pgq 2pgd

Description

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Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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