3FWN - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   DIMERIC 6-PHOSPHOGLUCONATE DEHYDROGENASE COMPLEXED WITH 6-PHOSPHOGLUCONATE AND 2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE

Authors :   Y. -Y. Chen, T. -P. Ko, L. -P. Lo, C. -H. Lin, A. H. -J. Wang

Date :   19 Jan 09 (Deposition) - 01 Sep 09 (Release) - 22 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A,B

Keywords :   Nadp, Pentose Phosphate Pathway, Oxidoreductase, 6-Phosphogluconate Dehydrogenase, 6-Phosphogluconate, Gluconate Utilization, Pentose Shunt (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. -Y. Chen, T. -P. Ko, W. -H. Chen, L. -P. Lo, C. -H. Lin, A. H. -J. Wang
Conformational Changes Associated With Cofactor/Substrate Binding Of 6-Phosphogluconate Dehydrogenase From Escherichi Coli And Klebsiella Pneumoniae: Implications For Enzyme Mechanism
J. Struct. Biol. V. 169 25 2010
PubMed-ID: 19686854 | Reference-DOI: 10.1016/J.JSB.2009.08.006

Molecule 1 - 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING
	Chains	:	A, B
	EC Number	:	1.1.1.44
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	GND
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K-12

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	6PG	2	Ligand/Ion	6-PHOSPHOGLUCONIC ACID
2	ATR	1	Ligand/Ion	2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:128 , GLY A:129 , GLY A:130 , LYS A:183 , HIS A:186 , ASN A:187 , GLU A:190 , TYR A:191 , ASN A:259 , LYS A:260 , ARG A:287 , ILE A:365 , HOH A:517 , HOH A:646 , HOH A:680 , HOH A:912 , HOH A:967 , ARG B:445 , PHE B:448 , HIS B:451	BINDING SITE FOR RESIDUE 6PG A 2002
2	AC2	SOFTWARE	ASN A:247 , MET B:11 , ALA B:12 , ASN B:33 , ARG B:34 , SER B:35 , LYS B:38 , VAL B:74 , LYS B:75 , GLY B:79 , LYS B:260 , HOH B:673 , HOH B:949 , HOH B:1098 , HOH B:1112 , HOH B:1113 , HOH B:1114 , HOH B:1408 , HOH B:1424 , HOH B:1571 , HOH B:1572 , HOH B:1669	BINDING SITE FOR RESIDUE ATR B 2000
3	AC3	SOFTWARE	ARG A:445 , PHE A:448 , HIS A:451 , ASN B:102 , SER B:128 , GLY B:129 , GLY B:130 , LYS B:183 , HIS B:186 , ASN B:187 , GLU B:190 , TYR B:191 , ASN B:259 , LYS B:260 , ARG B:287 , ILE B:365 , HOH B:638 , HOH B:692 , HOH B:867 , HOH B:1003 , HOH B:1577	BINDING SITE FOR RESIDUE 6PG B 2001

(no "SS Bond" information available for 3FWN)

Asymmetric/Biological Unit

No.	Residues
1	Thr A:66	-	Pro A:67
2	Thr B:66	-	Pro B:67

Asymmetric/Biological Unit (21, 42)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_6PGD_ECOLI_001 *	S	2	L	6PGD_ECOLI	---	---	A/B	S	2	L
02	UniProt	VAR_6PGD_ECOLI_002 *	F	32	Y	6PGD_ECOLI	---	---	A/B	F	32	Y
03	UniProt	VAR_6PGD_ECOLI_003 *	T	39	Q	6PGD_ECOLI	---	---	A/B	T	39	Q
04	UniProt	VAR_6PGD_ECOLI_004 *	V	52	D	6PGD_ECOLI	---	---	A/B	V	52	D
05	UniProt	VAR_6PGD_ECOLI_005 *	Y	55	F	6PGD_ECOLI	---	---	A/B	Y	55	F
06	UniProt	VAR_6PGD_ECOLI_006 *	N	102	K	6PGD_ECOLI	---	---	A/B	N	102	K
07	UniProt	VAR_6PGD_ECOLI_007 *	A	117	S	6PGD_ECOLI	---	---	A/B	A	117	S
08	UniProt	VAR_6PGD_ECOLI_008 *	V	170	F	6PGD_ECOLI	---	---	A/B	V	170	F
09	UniProt	VAR_6PGD_ECOLI_009 *	A	175	S	6PGD_ECOLI	---	---	A/B	A	175	S
10	UniProt	VAR_6PGD_ECOLI_010 *	N	209	S	6PGD_ECOLI	---	---	A/B	N	209	S
11	UniProt	VAR_6PGD_ECOLI_011 *	T	211	S	6PGD_ECOLI	---	---	A/B	T	211	S
12	UniProt	VAR_6PGD_ECOLI_012 *	A	216	T	6PGD_ECOLI	---	---	A/B	A	216	T
13	UniProt	VAR_6PGD_ECOLI_013 *	D	294	E	6PGD_ECOLI	---	---	A/B	D	294	E
14	UniProt	VAR_6PGD_ECOLI_014 *	A	308	G	6PGD_ECOLI	---	---	A/B	A	308	G
15	UniProt	VAR_6PGD_ECOLI_015 *	D	313	N	6PGD_ECOLI	---	---	A/B	D	313	N
16	UniProt	VAR_6PGD_ECOLI_016 *	A	315	G	6PGD_ECOLI	---	---	A/B	A	315	G
17	UniProt	VAR_6PGD_ECOLI_017 *	L	325	Q	6PGD_ECOLI	---	---	A/B	L	325	Q
18	UniProt	VAR_6PGD_ECOLI_018 *	I	330	S	6PGD_ECOLI	---	---	A/B	I	330	S
19	UniProt	VAR_6PGD_ECOLI_019 *	D	350	A	6PGD_ECOLI	---	---	A/B	D	350	A
20	UniProt	VAR_6PGD_ECOLI_020 *	Q	369	R	6PGD_ECOLI	---	---	A/B	Q	369	R
21	UniProt	VAR_6PGD_ECOLI_021 *	S	422	A	6PGD_ECOLI	---	---	A/B	S	422	A
	* ID not provided by source

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

Asymmetric/Biological Unit (1, 2)

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

(no "Exon" information available for 3FWN)

Asymmetric/Biological 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:467
 aligned with 6PGD_ECOLI | P00350 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:467
                                    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       
           6PGD_ECOLI     2 SKQQIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAENPGKKLVPYYTVKEFVESLETPRRILLMVKAGAGTDAAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGFNFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILTKIAAVAEDGEPCVTYIGADGAGHYVKMVHNGIEYGDMQLIAEAYSLLKGGLNLTNEELAQTFTEWNNGELSSYLIDITKDIFTKKDEDGNYLVDVILDEAANKGTGKWTSQSALDLGEPLSLITESVFARYISSLKDQRVAASKVLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWDLNYGEIAKIFRAGCIIRAQFLQKITDAYAENPQIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPVPTFSAAVAYYDSYRAAVLPANLIQAQRDYFGAHTYKRIDKEGVFHTEWLD 468
               SCOP domains d3fwna1 A:2-176 automated matches                                                                                                                                              d3fwna2 A:177-468 automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3fwnA01 A:2-180 NAD(P)-binding Rossmann-like Domain                                                                                                                                3fwnA02 A:181-434 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                                                                                                                   3fwnA03 A:435-468                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhh....eeee..hhhhhhhhhhhh....eee..hhhhhhhh.....eeee....hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...hhhhhhhhhhh........hhhhhh.......hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..ee......ee...... Sec.struct. author
                 SAPs(SNPs) L-----------------------------Y------Q------------D--F----------------------------------------------K--------------S----------------------------------------------------F----S---------------------------------S-S----T-----------------------------------------------------------------------------E-------------G----N-G---------Q----S-------------------A------------------R----------------------------------------------------A---------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------6PGD         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fwn A   2 SKQQIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAENPGKKLVPYYTVKEFVESLETPRRILLMVKAGAGTDAAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGFNFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILTKIAAVAEDGEPCVTYIGADGAGHYVKMVHNGIEYGDMQLIAEAYSLLKGGLNLTNEELAQTFTEWNNGELSSYLIDITKDIFTKKDEDGNYLVDVILDEAANKGTGKWTSQSALDLGEPLSLITESVFARYISSLKDQRVAASKVLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWDLNYGEIAKIFRAGCIIRAQFLQKITDAYAENPQIANLLLAPYFKQIADDYQQALRDVVAYAVQIGIPVPTFSAAVAYYDSYRAAVLPANLIQAQRDYFGAHTYKRIDKEGVFHTEWLD 468
                                    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

Chain B from PDB  Type:PROTEIN  Length:467
 aligned with 6PGD_ECOLI | P00350 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:467
                                    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       
           6PGD_ECOLI     2 SKQQIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAENPGKKLVPYYTVKEFVESLETPRRILLMVKAGAGTDAAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGFNFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILTKIAAVAEDGEPCVTYIGADGAGHYVKMVHNGIEYGDMQLIAEAYSLLKGGLNLTNEELAQTFTEWNNGELSSYLIDITKDIFTKKDEDGNYLVDVILDEAANKGTGKWTSQSALDLGEPLSLITESVFARYISSLKDQRVAASKVLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWDLNYGEIAKIFRAGCIIRAQFLQKITDAYAENPQIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPVPTFSAAVAYYDSYRAAVLPANLIQAQRDYFGAHTYKRIDKEGVFHTEWLD 468
               SCOP domains d3fwnb1 B:2-176 automated matches                                                                                                                                              d3fwnb2 B:177-468 automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3fwnB01 B:2-180 NAD(P)-binding Rossmann-like Domain                                                                                                                                3fwnB02 B:181-434 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                                                                                                                   3fwnB03 B:435-468                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhh....eee..hhhhhhhh.....eeee....hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhh.eeeeeehhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhh........hhhhh........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh........hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) L-----------------------------Y------Q------------D--F----------------------------------------------K--------------S----------------------------------------------------F----S---------------------------------S-S----T-----------------------------------------------------------------------------E-------------G----N-G---------Q----S-------------------A------------------R----------------------------------------------------A---------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------6PGD         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fwn B   2 SKQQIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAENPGKKLVPYYTVKEFVESLETPRRILLMVKAGAGTDAAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGFNFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILTKIAAVAEDGEPCVTYIGADGAGHYVKMVHNGIEYGDMQLIAEAYSLLKGGLNLTNEELAQTFTEWNNGELSSYLIDITKDIFTKKDEDGNYLVDVILDEAANKGTGKWTSQSALDLGEPLSLITESVFARYISSLKDQRVAASKVLSGPQAQPAGDKAEFIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWDLNYGEIAKIFRAGCIIRAQFLQKITDAYAENPQIANLLLAPYFKQIADDYQQALRDVVAYAVQIGIPVPTFSAAVAYYDSYRAAVLPANLIQAQRDYFGAHTYKRIDKEGVFHTEWLD 468
                                    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

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 '\|'

(no "Pfam Domain" information available for 3FWN)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (6PGD_ECOLI | P00350)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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+.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Thr A:66 - Pro A:67	[ RasMol ]
		Thr B:66 - Pro B:67	[ RasMol ]

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	3fwn
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	1.1.1.44
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	6PGD_ECOLI \| P00350	:	2zya 2zyd

2zya	MODEL FOR MOLECULAR REPLACEMENT
2zyg
3fwd

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (21, 42)

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Exons (0, 0)

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