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Title :   THE CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE KINASE/PHOSPHATASE FROM E. COLI

Authors :   J. Zheng, Z. Jia, Montreal-Kingston Bacterial Structural Genomic Initiative (Bsgi)

Date :   29 Sep 08 (Deposition) - 14 Apr 10 (Release) - 30 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Kinase Phosphatase, Atp-Binding, Glyoxylate Bypass, Kinase, Nucleotide-Binding, Protein Phosphatase, Tricarboxylic Acid Cycle, Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Transferase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Zheng, Z. Jia
Structure Of The Bifunctional Isocitrate Dehydrogenase Kinase/Phosphatase.
Nature V. 465 961 2010
PubMed-ID: 20505668 | Reference-DOI: 10.1038/NATURE09088

Molecule 1 - ISOCITRATE DEHYDROGENASE KINASE/PHOSPHATASE
	Chains	:	A, B
	EC Number	:	2.7.11.5, 3.1.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ACEK, ECS4934, Z5602
	Organism Taxid	:	83334
	Strain	:	K-12
	Synonym	:	IDH KINASE/PHOSPHATASE, IDHK/P

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:104 , SER A:105 , HIS A:113 , LEU A:116 , LYS A:291 , LYS A:294 , THR A:295 , TYR A:298 , GLU A:376 , ASN A:377	BINDING SITE FOR RESIDUE AMP A 1604
2	AC2	SOFTWARE	PRO A:316 , GLY A:317 , ILE A:318 , VAL A:322 , MET A:323 , VAL A:325 , LYS A:336 , GLU A:416 , ARG A:417 , ARG A:418 , MET A:419 , PRO A:421 , ASN A:462 , TYR A:474 , ASP A:475 , ASP A:477 , GLU A:478 , MG A:1606	BINDING SITE FOR RESIDUE ATP A 1605
3	AC3	SOFTWARE	ASN A:462 , ASP A:475 , ATP A:1605	BINDING SITE FOR RESIDUE MG A 1606
4	AC4	SOFTWARE	ASN B:104 , SER B:105 , HIS B:113 , LEU B:116 , LYS B:291 , LYS B:294 , THR B:295 , TYR B:298 , GLU B:376 , ASN B:377 , HOH B:580	BINDING SITE FOR RESIDUE AMP B 1604
5	AC5	SOFTWARE	PRO B:316 , GLY B:317 , ILE B:318 , VAL B:322 , MET B:323 , VAL B:325 , VAL B:334 , LYS B:336 , GLU B:416 , ARG B:417 , ARG B:418 , MET B:419 , PRO B:421 , ASN B:462 , TYR B:474 , ASP B:475 , ASP B:477 , GLU B:478 , HOH B:594 , MG B:1606	BINDING SITE FOR RESIDUE ATP B 1605
6	AC6	SOFTWARE	ASN B:462 , ASP B:475 , ATP B:1605	BINDING SITE FOR RESIDUE MG B 1606

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

(no "Cis Peptide Bond" information available for 3EPS)

(no "SAP(SNP)/Variant" information available for 3EPS)

(no "PROSITE Motif" information available for 3EPS)

(no "Exon" information available for 3EPS)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:566
 aligned with ACEK_ECO57 | Q8X607 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:573
                                    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       481       491       501       511       521       531       541       551       561       571   
           ACEK_ECO57     2 PRGLELLIAQTILQGFDAQYGRFLEVTSGAQQRFEQADWHAVQQAMKNRIHLYDHHVGLVVEQLRCITNGQSTDAEFLLRVKEHYTRLLPDYPRFEIAESFFNSVYCRLFDHRSLTPERLFIFSSQPERRFRTIPRPLAKDFHPDHGWESLLMRVISDLPLRLHWQNKSRDIHYIIRHLTETLGPENLSKSHLQVANELFYRNKAAWLVGKLITPSGTLPFLLPIHQTDDGELFIDTCLTTTAEASIVFGFARSYFMVYAPLPAALVEWLREILPGKTTAELYMAIGCQKHAKTESYREYLVYLQGCNEQFIEAPGIRGMVMLVFTLPGFDRVFKVIKDKFAPQKEMSAAHVRACYQLVKEHDRVGRMADTQEFENFVLEKRHISPALMELLLQEAAEKITDLGEQIVIRHLYIERRMVPLNIWLEQVEGQQLRDAIEEYGNAIRQLAAANIFPGDMLFKNFGVTRHGRVVFYDYDEICYMTEVNFRDIPPPRYPEDELASEPWYSVSPGDVFPEEFRHWLCADPRIGPLFEEMHADLFRADYWRALQNRIREGHVEDVYAYRRRQRFSVRYG 574
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh............................eeee.......hhhhhhhh......ee.hhhhhhhhhhhhhhhhhhhhhhh..eeeee...eee..eeeeeeeeee..eeeeeeeeeee....eeee.....hhhhhhhhh............hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee........eeeee.....eeeeee..........hhhhhhhhhhhhhh..........eeeeeeeee.hhhhhhhhhhhhhhh...eeee..eeeeeeeeeee..eehhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee.hhhhhee....ee.........-------........ee..hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eps A   2 PRGLELLIAQTILQGFDAQYGRFLEVTSGAQQRFEQADWHAVQQAMKNRIHLYDHHVGLVVEQLRCITNGQSTDAEFLLRVKEHYTRLLPDYPRFEIAESFFNSVYCRLFDHRSLTPERLFIFSSQPERRFRTIPRPLAKDFHPDHGWESLLMRVISDLPLRLHWQNKSRDIHYIIRHLTETLGPENLSKSHLQVANELFYRNKAAWLVGKLITPSGTLPFLLPIHQTDDGELFIDTCLTTTAEASIVFGFARSYFMVYAPLPAALVEWLREILPGKTTAELYMAIGCQKHAKTESYREYLVYLQGCNEQFIEAPGIRGMVMLVFTLPGFDRVFKVIKDKFAPQKEMSAAHVRACYQLVKEHDRVGRMADTQEFENFVLEKRHISPALMELLLQEAAEKITDLGEQIVIRHLYIERRMVPLNIWLEQVEGQQLRDAIEEYGNAIRQLAAANIFPGDMLFKNFGVTRHGRVVFYDYDEICYMTEVNFRDIPPPRYP-------PWYSVSPGDVFPEEFRHWLCADPRIGPLFEEMHADLFRADYWRALQNRIREGHVEDVYAYRRRQRFSVRYG 574
                                    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       481       491    |    -  |    511       521       531       541       551       561       571   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        496     504

Chain B from PDB  Type:PROTEIN  Length:559
 aligned with ACEK_ECO57 | Q8X607 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:573
                                    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       481       491       501       511       521       531       541       551       561       571   
           ACEK_ECO57     2 PRGLELLIAQTILQGFDAQYGRFLEVTSGAQQRFEQADWHAVQQAMKNRIHLYDHHVGLVVEQLRCITNGQSTDAEFLLRVKEHYTRLLPDYPRFEIAESFFNSVYCRLFDHRSLTPERLFIFSSQPERRFRTIPRPLAKDFHPDHGWESLLMRVISDLPLRLHWQNKSRDIHYIIRHLTETLGPENLSKSHLQVANELFYRNKAAWLVGKLITPSGTLPFLLPIHQTDDGELFIDTCLTTTAEASIVFGFARSYFMVYAPLPAALVEWLREILPGKTTAELYMAIGCQKHAKTESYREYLVYLQGCNEQFIEAPGIRGMVMLVFTLPGFDRVFKVIKDKFAPQKEMSAAHVRACYQLVKEHDRVGRMADTQEFENFVLEKRHISPALMELLLQEAAEKITDLGEQIVIRHLYIERRMVPLNIWLEQVEGQQLRDAIEEYGNAIRQLAAANIFPGDMLFKNFGVTRHGRVVFYDYDEICYMTEVNFRDIPPPRYPEDELASEPWYSVSPGDVFPEEFRHWLCADPRIGPLFEEMHADLFRADYWRALQNRIREGHVEDVYAYRRRQRFSVRYG 574
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh............................ee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh...eeee...eee..eee.eeeeee..eeeeee..eee.....eee.....hhhhhhhhh............hhhhhhhhhh......hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....ee........eeeee.....eeeeee..........hhhhhhhhhhhhhh.........eeeeeeeeee.hhhhhhhhhhhhhhh...eee...eeeeeeeeeee..eehhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee.hhhhhee.hhhee....--------------......eehhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eps B   2 PRGLELLIAQTILQGFDAQYGRFLEVTSGAQQRFEQADWHAVQQAMKNRIHLYDHHVGLVVEQLRCITNGQSTDAEFLLRVKEHYTRLLPDYPRFEIAESFFNSVYCRLFDHRSLTPERLFIFSSQPERRFRTIPRPLAKDFHPDHGWESLLMRVISDLPLRLHWQNKSRDIHYIIRHLTETLGPENLSKSHLQVANELFYRNKAAWLVGKLITPSGTLPFLLPIHQTDDGELFIDTCLTTTAEASIVFGFARSYFMVYAPLPAALVEWLREILPGKTTAELYMAIGCQKHAKTESYREYLVYLQGCNEQFIEAPGIRGMVMLVFTLPGFDRVFKVIKDKFAPQKEMSAAHVRACYQLVKEHDRVGRMADTQEFENFVLEKRHISPALMELLLQEAAEKITDLGEQIVIRHLYIERRMVPLNIWLEQVEGQQLRDAIEEYGNAIRQLAAANIFPGDMLFKNFGVTRHGRVVFYDYDEICYMTEVNFRDIP--------------YSVSPGDVFPEEFRHWLCADPRIGPLFEEMHADLFRADYWRALQNRIREGHVEDVYAYRRRQRFSVRYG 574
                                    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       481       491         -    |  511       521       531       541       551       561       571   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   491            506

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 "SCOP Domain" information available for 3EPS)

(no "CATH Domain" information available for 3EPS)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (ACEK_ECO57 | Q8X607)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008772	[isocitrate dehydrogenase (NADP+)] kinase activity	Catalysis of the reaction: ATP + (isocitrate dehydrogenase (NADP)) = ADP + (isocitrate dehydrogenase (NADP)) phosphate.
	GO:0101014	[isocitrate dehydrogenase (NADP+)] phosphatase activity	Catalysis of the reaction: [isocitrate dehydrogenase] phosphate + H2O = [isocitrate dehydrogenase] + phosphate.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0004721	phosphoprotein phosphatase activity	Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
	GO:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	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:0006097	glyoxylate cycle	A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0006099	tricarboxylic acid cycle	A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
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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