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Title :   CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE FROM BACILLUS SUBTILIS

Authors :   S. K. Singh, K. Matsuno, D. C. Laporte, L. J. Banaszak

Date :   19 Dec 00 (Deposition) - 25 Jul 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Glyoxylate Bypass, Bsidh, Tricarboxylic Acid Cycle, Oxidoreductase, Protein Phosphorylation, Nadp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. K. Singh, K. Matsuno, D. C. Laporte, L. J. Banaszak
Crystal Structure Of Bacillus Subtilis Isocitrate Dehydrogenase At 1. 55 A. Insights Into The Nature Of Substrate Specificity Exhibited By Escherichia Coli Isocitrate Dehydrogenase Kinase/Phosphatase.
J. Biol. Chem. V. 276 26154 2001
PubMed-ID: 11290745 | Reference-DOI: 10.1074/JBC.M101191200
(for further references see the PDB file header)

Molecule 1 - ISOCITRATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.42
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKM14
	Expression System Strain	:	KME44
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CITC
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Synonym	:	OXALOSUCCINATE DECARBOXYLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 11)

No.	Name	Count	Type	Full Name
1	CIT	2	Ligand/Ion	CITRIC ACID
2	CME	2	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
3	PGO	5	Ligand/Ion	S-1,2-PROPANEDIOL
4	PGR	2	Ligand/Ion	R-1,2-PROPANEDIOL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:96 , SER A:104 , ASN A:106 , ARG A:110 , ARG A:144 , TYR A:151 , THR A:344 , HIS A:345 , HOH A:1438 , HOH A:1501 , LYS B:221 , ASN B:223 , ILE B:224	BINDING SITE FOR RESIDUE CIT A 425
2	AC2	SOFTWARE	LYS A:221 , ASN A:223 , ILE A:224 , PGR A:907 , THR B:96 , SER B:104 , ASN B:106 , ARG B:110 , ARG B:144 , TYR B:151 , ASP B:311	BINDING SITE FOR RESIDUE CIT B 825
3	AC3	SOFTWARE	PRO A:121 , VAL A:122 , ARG A:123 , PHE A:125 , VAL A:321 , ILE A:326 , PRO A:328 , PGO A:902	BINDING SITE FOR RESIDUE PGO A 901
4	AC4	SOFTWARE	ARG A:123 , PGO A:901 , HOH A:1369	BINDING SITE FOR RESIDUE PGO A 902
5	AC5	SOFTWARE	HOH A:1105 , ARG B:134 , ASP B:137 , THR B:295 , HOH B:1592	BINDING SITE FOR RESIDUE PGO B 903
6	AC6	SOFTWARE	TRP B:251 , TYR B:254 , GLN B:270 , HOH B:1463	BINDING SITE FOR RESIDUE PGO B 904
7	AC7	SOFTWARE	PRO B:121 , ARG B:123 , HOH B:1338 , HOH B:1489 , HOH B:1579 , HOH B:1589	BINDING SITE FOR RESIDUE PGO B 905
8	AC8	SOFTWARE	TYR A:237 , TRP A:251 , ALA A:252 , ASP A:255 , ASP A:283 , HOH A:1215	BINDING SITE FOR RESIDUE PGR A 906
9	AC9	SOFTWARE	LYS A:221 , ASN A:223 , ILE A:285 , ASP A:287 , ILE A:288 , CIT B:825	BINDING SITE FOR RESIDUE PGR A 907

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

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IDH_IMDH	PS00470	Isocitrate and isopropylmalate dehydrogenases signature.	IDH_BACSU	307-326	2	A:307-326 B:307-326

(no "Exon" information available for 1HQS)

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
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Chain A from PDB  Type:PROTEIN  Length:423
 aligned with IDH_BACSU | P39126 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:423
                                    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   
            IDH_BACSU     1 MAQGEKITVSNGVLNVPNNPIIPFIEGDGTGPDIWNAASKVLEAAVEKAYKGEKKITWKEVYAGEKAYNKTGEWLPAETLDVIREYFIAIKGPLTTPVGGGIRSLNVALRQELDLFVCLRPVRYFTGVPSPVKRPEDTDMVIFRENTEDIYAGIEYAKGSEEVQKLISFLQNELNVNKIRFPETSGIGIKPVSEEGTSRLVRAAIDYAIEHGRKSVTLVHKGNIMKFTEGAFKNWGYELAEKEYGDKVFTWAQYDRIAEEQGKDAANKAQSEAEAAGKIIIKDSIADIFLQQILTRPNEFDVVATMNLNGDYISDALAAQVGGIGIAPGANINYETGHAIFEATHGTAPKYAGLDKVNPSSVILSGVLLLEHLGWNEAADLVIKSMEKTIASKVVTYDFARLMDGATEVKCSEFGEELIKNMD 423
               SCOP domains d1hqsa_ A: Isocitrate dehydrogenase, ICDH                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1hqsA00 A:1-423 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eee.....eeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhh...hhhhhhhhhhhheeee............hhhhhhhhhh......eeee..........hhhh.eeeeee...hhhhhh.ee...hhhhhhhhhhhhhhh......hhh.eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhh......eeeee......eeeee....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhh.....ee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hqs A   1 MAQGEKITVSNGVLNVPNNPIIPFIEGDGTGPDIWNAASKVLEAAVEKAYKGEKKITWKEVYAGEKAYNKTGEWLPAETLDVIREYFIAIKGPLTTPVGGGIRSLNVALRQELDLFVcLRPVRYFTGVPSPVKRPEDTDMVIFRENTEDIYAGIEYAKGSEEVQKLISFLQNELNVNKIRFPETSGIGIKPVSEEGTSRLVRAAIDYAIEHGRKSVTLVHKGNIMKFTEGAFKNWGYELAEKEYGDKVFTWAQYDRIAEEQGKDAANKAQSEAEAAGKIIIKDSIADIFLQQILTRPNEFDVVATMNLNGDYISDALAAQVGGIGIAPGANINYETGHAIFEATHGTAPKYAGLDKVNPSSVILSGVLLLEHLGWNEAADLVIKSMEKTIASKVVTYDFARLMDGATEVKCSEFGEELIKNMD 423
                                    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   
                                                                                                                                               118-CME

Chain B from PDB  Type:PROTEIN  Length:423
 aligned with IDH_BACSU | P39126 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:423
                                    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   
            IDH_BACSU     1 MAQGEKITVSNGVLNVPNNPIIPFIEGDGTGPDIWNAASKVLEAAVEKAYKGEKKITWKEVYAGEKAYNKTGEWLPAETLDVIREYFIAIKGPLTTPVGGGIRSLNVALRQELDLFVCLRPVRYFTGVPSPVKRPEDTDMVIFRENTEDIYAGIEYAKGSEEVQKLISFLQNELNVNKIRFPETSGIGIKPVSEEGTSRLVRAAIDYAIEHGRKSVTLVHKGNIMKFTEGAFKNWGYELAEKEYGDKVFTWAQYDRIAEEQGKDAANKAQSEAEAAGKIIIKDSIADIFLQQILTRPNEFDVVATMNLNGDYISDALAAQVGGIGIAPGANINYETGHAIFEATHGTAPKYAGLDKVNPSSVILSGVLLLEHLGWNEAADLVIKSMEKTIASKVVTYDFARLMDGATEVKCSEFGEELIKNMD 423
               SCOP domains d1hqsb_ B: Isocitrate dehydrogenase, ICDH                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1hqsB00 B:1-423 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eee.....eeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhh...hhhhhhhhhhhheeee............hhhhhhhhhh......eeee..........hhhh.eeeeee...hhhhhh.ee...hhhhhhhhhhhhhhh......hhh.eeeeeeeeehhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhh......eeeee......eeeee....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhh.....ee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hqs B   1 MAQGEKITVSNGVLNVPNNPIIPFIEGDGTGPDIWNAASKVLEAAVEKAYKGEKKITWKEVYAGEKAYNKTGEWLPAETLDVIREYFIAIKGPLTTPVGGGIRSLNVALRQELDLFVcLRPVRYFTGVPSPVKRPEDTDMVIFRENTEDIYAGIEYAKGSEEVQKLISFLQNELNVNKIRFPETSGIGIKPVSEEGTSRLVRAAIDYAIEHGRKSVTLVHKGNIMKFTEGAFKNWGYELAEKEYGDKVFTWAQYDRIAEEQGKDAANKAQSEAEAAGKIIIKDSIADIFLQQILTRPNEFDVVATMNLNGDYISDALAAQVGGIGIAPGANINYETGHAIFEATHGTAPKYAGLDKVNPSSVILSGVLLLEHLGWNEAADLVIKSMEKTIASKVVTYDFARLMDGATEVKCSEFGEELIKNMD 423
                                    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   
                                                                                                                                               118-CME

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: Isocitrate/Isopropylmalate dehydrogenase-like (143)

Superfamily: Isocitrate/Isopropylmalate dehydrogenase-like (143)

Family: Dimeric isocitrate & isopropylmalate dehydrogenases (102)

Protein domain: Isocitrate dehydrogenase, ICDH (27)

Bacillus subtilis [TaxId: 1423] (1)

1a	d1hqsa_	A:
1b	d1hqsb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

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Class: Alpha Beta (26913)

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

Topology: Isopropylmalate Dehydrogenase (91)

Homologous Superfamily: Isopropylmalate Dehydrogenase (91)

Bacillus subtilis. Organism_taxid: 1423. (2)

1a	1hqsA00	A:1-423
1b	1hqsB00	B:1-423

(no "Pfam Domain" information available for 1HQS)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (IDH_BACSU | P39126)

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:0004450	isocitrate dehydrogenase (NADP+) activity	Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	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: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: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.

Asymmetric/Biological Unit
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	1hqs
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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