4AJA - JenaLib

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Title :   3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE IN COMPLEX WITH ISOCITRATE, CALCIUM(II) AND THIONADP

Authors :   S. Goncalves, S. P. Miller, M. A. Carrondo, A. M. Dean, P. M. Matias

Date :   16 Feb 12 (Deposition) - 31 Oct 12 (Release) - 31 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Oxidoreductase, Oxidative Beta-Decarboxylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Goncalves, S. P. Miller, M. A. Carrondo, A. M. Dean, P. M. Matias
Induced Fit And The Catalytic Mechanism Of Isocitrate Dehydrogenase.
Biochemistry V. 51 7098 2012
PubMed-ID: 22891681 | Reference-DOI: 10.1021/BI300483W

Molecule 1 - NADP ISOCITRATE DEHYDROGENASE
	Chains	:	A
	EC Number	:	1.1.1.42
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 4)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	ICT	1	Ligand/Ion	ISOCITRIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION
4	TAP	1	Ligand/Ion	7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	ICT	2	Ligand/Ion	ISOCITRIC ACID
3	SO4	2	Ligand/Ion	SULFATE ION
4	TAP	2	Ligand/Ion	7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:58 , LEU A:103 , THR A:104 , THR A:105 , ASN A:115 , ILE A:281 , HIS A:339 , GLY A:340 , THR A:341 , ALA A:342 , TYR A:345 , ASN A:352 , TYR A:391 , ASP A:392 , ARG A:395 , ICT A:502 , HOH A:2169 , HOH A:2424 , HOH A:2425 , HOH A:2428 , HOH A:2429 , HOH A:2434 , HOH A:2476 , HOH A:2499 , HOH A:2500 , HOH A:2501 , HOH A:2502 , HOH A:2503 , HOH A:2504 , HOH A:2505	BINDING SITE FOR RESIDUE TAP A 501
2	AC2	SOFTWARE	SER A:113 , ASN A:115 , ARG A:119 , ARG A:129 , ARG A:153 , TYR A:160 , LYS A:230 , ASN A:232 , ASP A:283 , ASP A:307 , TAP A:501 , CA A:503 , HOH A:2171 , HOH A:2423 , HOH A:2500	BINDING SITE FOR RESIDUE ICT A 502
3	AC3	SOFTWARE	ASP A:283 , ASP A:307 , ASP A:311 , ICT A:502 , HOH A:2208 , HOH A:2411	BINDING SITE FOR RESIDUE CA A 503
4	AC4	SOFTWARE	VAL A:107 , GLY A:108 , GLY A:109 , GLY A:110 , ILE A:111 , LYS A:235 , HOH A:2177	BINDING SITE FOR RESIDUE SO4 A 504

(no "SS Bond" information available for 4AJA)

Asymmetric Unit

No.	Residues
1	Gly A:261	-	Pro A:262

(no "SAP(SNP)/Variant" information available for 4AJA)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IDH_IMDH	PS00470	Isocitrate and isopropylmalate dehydrogenases signature.	IDH_ECOLI	303-322	1	A:303-322

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IDH_IMDH	PS00470	Isocitrate and isopropylmalate dehydrogenases signature.	IDH_ECOLI	303-322	2	A:303-322

(no "Exon" information available for 4AJA)

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:415
 aligned with IDH_ECOLI | P08200 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:415
                                    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     
            IDH_ECOLI     2 ESKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLREEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGAFKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIACMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSAEMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM 416
               SCOP domains d4ajaa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eee..eee.....eeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhh.....hhhhhhhhhhhheeee............hhhhhhhhhh...eeeeeee..........hhhh.eeeeeee..hhhhhh.ee...hhhhhhhhhhhhhh.............ee....hhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhh.ee......eeee......eeeeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhh......eeeee....eeeee....hhhhh......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.eehhhhhh.....ee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aja A   2 ESKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLREEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGAFKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIACMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSAEMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM 416
                                    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

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

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

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: automated matches (45)

Escherichia coli [TaxId: 562] (5)

d4ajaa_

(no "CATH Domain" information available for 4AJA)

(no "Pfam Domain" information available for 4AJA)

Asymmetric Unit(hide GO term definitions)

Chain A (IDH_ECOLI | P08200)

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.
biological process
	GO:0022900	electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	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:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (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: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.
	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 Unit
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	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ICT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TAP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:261 - Pro A:262	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	4aja
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	1.1.1.42
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4aj3	3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE IN COMPLEX WITH ISOCITRATE, CALCIUM(II) AND NADP - THE PSEUDO-MICHAELIS COMPLEX
4ajb	3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE K100M MUTANT IN COMPLEX WITH ISOCITRATE, CALCIUM(II) AND THIONADP
4ajc	3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE K100M MUTANT IN COMPLEX WITH ALPHA-KETOGLUTARATE, CALCIUM(II ) AND ADENINE NUCLEOTIDE PHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

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