2D1C - JenaLib

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Title :   CRYSTAL STRUCTURE OF TT0538 PROTEIN FROM THERMUS THERMOPHILUS HB8

Authors :   N. K. Lokanath, N. Kunishima, Riken Structural Genomics/Proteomic Initiative (Rsgi)

Date :   15 Aug 05 (Deposition) - 10 Oct 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Dehydrogenase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. K. Lokanath, N. Kunishima
Crystal Structure Of Tt0538 Protein From Thermus Thermophilus Hb8
To Be Published
PubMed: search

Molecule 1 - ISOCITRATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.42
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8
	Synonym	:	OXALOSUCCINATE DECARBOXYLASE, IDH, NADP+, -SPECIFIC ICDH, IDP

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CIT	2	Ligand/Ion	CITRIC ACID
2	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:85 , PRO A:87 , LEU A:88 , GLU A:89 , THR A:90 , ASN A:100 , LEU A:261 , GLU A:277 , VAL A:279 , HIS A:280 , GLY A:281 , SER A:282 , ALA A:283 , LYS A:285 , TYR A:286 , ILE A:292 , ASN A:293 , ASP A:334 , CIT A:1585 , HOH A:1618 , HOH A:1717 , HOH A:1800 , HOH A:1810 , HOH A:1839 , HOH A:1975 , ASN B:193 , ILE B:222 , ASN B:225 , HIS B:228 , GLN B:229 , LYS B:232 , HOH B:1669 , HOH B:1975	BINDING SITE FOR RESIDUE NAP A 1002
2	AC2	SOFTWARE	ASN A:193 , ILE A:222 , ASN A:225 , GLN A:229 , LYS A:232 , HOH A:1625 , HOH A:1759 , LYS B:85 , PRO B:87 , LEU B:88 , GLU B:89 , THR B:90 , ASN B:100 , LEU B:261 , GLU B:277 , VAL B:279 , HIS B:280 , GLY B:281 , SER B:282 , ALA B:283 , LYS B:285 , TYR B:286 , ILE B:292 , ASN B:293 , ASP B:334 , CIT B:1586 , HOH B:1612 , HOH B:1687 , HOH B:1711 , HOH B:1745 , HOH B:1816 , HOH B:1840	BINDING SITE FOR RESIDUE NAP B 1003
3	AC3	SOFTWARE	THR A:90 , SER A:98 , ASN A:100 , ARG A:104 , ARG A:114 , ARG A:137 , TYR A:144 , ASP A:248 , NAP A:1002 , LYS B:191 , ASN B:193 , ASP B:224 , HOH B:1693 , HOH B:1854	BINDING SITE FOR RESIDUE CIT A 1585
4	AC4	SOFTWARE	LYS A:191 , ASN A:193 , ASP A:224 , THR B:90 , SER B:98 , ASN B:100 , ARG B:104 , ARG B:114 , ARG B:137 , TYR B:144 , ASP B:248 , NAP B:1003 , HOH B:1688 , HOH B:1698	BINDING SITE FOR RESIDUE CIT B 1586

(no "SS Bond" information available for 2D1C)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:431	-	Pro A:432
2	Tyr B:431	-	Pro B:432

(no "SAP(SNP)/Variant" information available for 2D1C)

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_THET8	244-263	2	A:244-263 B:244-263

(no "Exon" information available for 2D1C)

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:495
 aligned with IDH_THET8 | P33197 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:495
                                    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     
            IDH_THET8     2 PLITTETGKKMHVLEDGRKLITVIPGDGIGPECVEATLKVLEAAKAPLAYEVREAGASVFRRGIASGVPQETIESIRKTRVVLKGPLETPVGYGEKSANVTLRKLFETYANVRPVREFPNVPTPYAGRGIDLVVVRENVEDLYAGIEHMQTPSVAQTLKLISWKGSEKIVRFAFELARAEGRKKVHCATKSNIMKLAEGTLKRAFEQVAQEYPDIEAVHIIVDNAAHQLVKRPEQFEVIVTTNMNGDILSDLTSGLIGGLGFAPSANIGNEVAIFEAVHGSAPKYAGKNVINPTAVLLSAVMMLRYLEEFATADLIENALLYTLEEGRVLTGDVVGYDRGAKTTEYTEAIIQNLGKTPRKTQVRGYKPFRLPQVDGAIAPIVPRSRRVVGVDVFVETNLLPEALGKALEDLAAGTPFRLKMISNRGTQVYPPTGGLTDLVDHYRCRFLYTGEGEAKDPEILDLVSRVASRFRWMHLEKLQEFDGEPGFTKAQGED 496
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2d1cA01 A:2-385 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                   --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeee.....eeeeee....hhhhhhhhhhhhhhhh...eeeee...hhhhhh.......hhhhhhhhhhhheeee............hhhhhhhhhh...eeeeeee..............eeeeeee...hhhhh.eeeee..eeeeeeeeehhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhh...hhhh.eeeee....eeeee...............hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhh.....hhhhhhhhhhhh...................hhhhh........eeeeeeeeeee...hhhhhhhhhhhhhh...eeeeeeee..eeee...........eeeeeeee......hhhhhhhhhhhhhh..eeeeeeeeeee..ee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d1c A   2 PLITTETGKKMHVLEDGRKLITVIPGDGIGPECVEATLKVLEAAKAPLAYEVREAGASVFRRGIASGVPQETIESIRKTRVVLKGPLETPVGYGEKSANVTLRKLFETYANVRPVREFPNVPTPYAGRGIDLVVVRENVEDLYAGIEHMQTPSVAQTLKLISWKGSEKIVRFAFELARAEGRKKVHCATKSNIMKLAEGTLKRAFEQVAQEYPDIEAVHIIVDNAAHQLVKRPEQFEVIVTTNMNGDILSDLTSGLIGGLGFAPSANIGNEVAIFEAVHGSAPKYAGKNVINPTAVLLSAVMMLRYLEEFATADLIENALLYTLEEGRVLTGDVVGYDRGAKTTEYTEAIIQNLGKTPRKTQVRGYKPFRLPQVDGAIAPIVPRSRRVVGVDVFVETNLLPEALGKALEDLAAGTPFRLKMISNRGTQVYPPTGGLTDLVDHYRCRFLYTGEGEAKDPEILDLVSRVASRFRWMHLEKLQEFDGEPGFTKAQGED 496
                                    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

Chain B from PDB  Type:PROTEIN  Length:495
 aligned with IDH_THET8 | P33197 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:495
                                    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     
            IDH_THET8     2 PLITTETGKKMHVLEDGRKLITVIPGDGIGPECVEATLKVLEAAKAPLAYEVREAGASVFRRGIASGVPQETIESIRKTRVVLKGPLETPVGYGEKSANVTLRKLFETYANVRPVREFPNVPTPYAGRGIDLVVVRENVEDLYAGIEHMQTPSVAQTLKLISWKGSEKIVRFAFELARAEGRKKVHCATKSNIMKLAEGTLKRAFEQVAQEYPDIEAVHIIVDNAAHQLVKRPEQFEVIVTTNMNGDILSDLTSGLIGGLGFAPSANIGNEVAIFEAVHGSAPKYAGKNVINPTAVLLSAVMMLRYLEEFATADLIENALLYTLEEGRVLTGDVVGYDRGAKTTEYTEAIIQNLGKTPRKTQVRGYKPFRLPQVDGAIAPIVPRSRRVVGVDVFVETNLLPEALGKALEDLAAGTPFRLKMISNRGTQVYPPTGGLTDLVDHYRCRFLYTGEGEAKDPEILDLVSRVASRFRWMHLEKLQEFDGEPGFTKAQGED 496
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2d1cB01 B:2-385 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                   --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eeee.....eeeeee....hhhhhhhhhhhhhhhh...eeeee...hhhhhh.......hhhhhhhhhhhheeee............hhhhhhhhhh...eeeeeee..............eeeeeee...hhhhh.eeeee..eeeeeeeeehhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhh...hhhh.eeeee....eeeee....hhhhh......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhh.....hhhhhhhhhhhh...................hhhhh........eeeeeeeeeee...hhhhhhhhhhhhhh...eeeeeeee..eeee...........eeeeeeee......hhhhhhhhhhhhhh..eeeeeeeeeee..ee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d1c B   2 PLITTETGKKMHVLEDGRKLITVIPGDGIGPECVEATLKVLEAAKAPLAYEVREAGASVFRRGIASGVPQETIESIRKTRVVLKGPLETPVGYGEKSANVTLRKLFETYANVRPVREFPNVPTPYAGRGIDLVVVRENVEDLYAGIEHMQTPSVAQTLKLISWKGSEKIVRFAFELARAEGRKKVHCATKSNIMKLAEGTLKRAFEQVAQEYPDIEAVHIIVDNAAHQLVKRPEQFEVIVTTNMNGDILSDLTSGLIGGLGFAPSANIGNEVAIFEAVHGSAPKYAGKNVINPTAVLLSAVMMLRYLEEFATADLIENALLYTLEEGRVLTGDVVGYDRGAKTTEYTEAIIQNLGKTPRKTQVRGYKPFRLPQVDGAIAPIVPRSRRVVGVDVFVETNLLPEALGKALEDLAAGTPFRLKMISNRGTQVYPPTGGLTDLVDHYRCRFLYTGEGEAKDPEILDLVSRVASRFRWMHLEKLQEFDGEPGFTKAQGED 496
                                    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

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 2D1C)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Isopropylmalate Dehydrogenase (91)

Homologous Superfamily: Isopropylmalate Dehydrogenase (91)

Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. (6)

1a	2d1cA01	A:2-385
1b	2d1cB01	B:2-385

(no "Pfam Domain" information available for 2D1C)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (IDH_THET8 | P33197)

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: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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	Cis Peptide Bonds
		Tyr A:431 - Pro A:432	[ RasMol ]
		Tyr B:431 - Pro B:432	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

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SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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