2Y41 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS - COMPLEX WITH IPM AND MN

Authors :   E. Graczer, A. Merlin, R. K. Singh, K. Manikandan, P. Zavodsky, M. S. Wei

Date :   04 Jan 11 (Deposition) - 19 Jan 11 (Release) - 18 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Oxidoreductase, Leub, Leucine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Graczer, A. Merli, R. K. Singh, M. Karuppasamy, P. Zavodszky, M. S. Weiss, M. Vas
Atomic Level Description Of The Domain Closure In A Dimeric Enzyme: Thermus Thermophilus 3-Isopropylmalate Dehydrogenase.
Mol. Biosyst. V. 7 1646 2011
PubMed-ID: 21387033 | Reference-DOI: 10.1039/C0MB00346H
(for further references see the PDB file header)

Molecule 1 - 3-ISOPROPYLMALATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.85
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET21C
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Other Details	:	ADDITIONAL AMINO ACIDS- N-TERMINAL MAS. C- TERMINAL AAALEHHHHHH
	Synonym	:	ISOPROPYLMALATE DEHYDROGENASE, 3-IPM-DH, BETA-IPM DEHYDROGENASE, IMDH, IPMDH

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	IPM	2	Ligand/Ion	3-ISOPROPYLMALIC ACID
2	MN	4	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:94 , ARG A:104 , ARG A:132 , TYR A:139 , ASP A:241 , MN A:999 , HOH A:2116 , HOH A:2117 , LYS B:185 , VAL B:188 , ASP B:217	BINDING SITE FOR RESIDUE IPM A 800
2	AC2	SOFTWARE	ASP A:241 , IPM A:800 , HOH A:2118 , HOH A:2119 , LYS B:185 , ASP B:217	BINDING SITE FOR RESIDUE MN A 999
3	AC3	SOFTWARE	LYS A:185 , VAL A:188 , ASP A:217 , ARG B:94 , ARG B:104 , ARG B:132 , TYR B:139 , ASP B:241 , MN B:999 , HOH B:2078 , HOH B:2080 , HOH B:2081	BINDING SITE FOR RESIDUE IPM B 800
4	AC4	SOFTWARE	ASP A:217 , ASP B:241 , ASP B:245 , IPM B:800 , HOH B:2080 , HOH B:2081	BINDING SITE FOR RESIDUE MN B 999
5	AC5	SOFTWARE	HOH B:2082 , HOH B:2083 , HOH B:2084 , HOH B:2085	BINDING SITE FOR RESIDUE MN B1000
6	AC6	SOFTWARE	HOH B:2086 , HOH B:2087 , HOH B:2088 , HOH B:2089 , HOH B:2090	BINDING SITE FOR RESIDUE MN B1001

(no "SS Bond" information available for 2Y41)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:142	-	Pro A:143
2	Glu B:142	-	Pro B:143

(no "SAP(SNP)/Variant" information available for 2Y41)

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.	LEU3_THET8	237-256	2	A:237-256 B:237-256

(no "Exon" information available for 2Y41)

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:347
 aligned with LEU3_THET8 | Q5SIY4 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:347
                             1                                                                                                                                                                                                                                                                                                                                                     345 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339     | 
           LEU3_THET8     - -MKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFEAARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVLRHLA-   -
               SCOP domains d2y41a_ A: automated matches                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh...hhhhhhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhhhhhhh...eeeeeee....hhhhh..hhhhhh..eeeeeee..hhhhh....ee...eeeeeeeeehhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhh...hhhhh..eee.....ee......hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y41 A   0 SMKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFEAARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVLRHLAA 346
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339

Chain B from PDB  Type:PROTEIN  Length:347
 aligned with LEU3_THET8 | Q5SIY4 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:347
                             1                                                                                                                                                                                                                                                                                                                                                     345 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339     | 
           LEU3_THET8     - -MKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFEAARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVLRHLA-   -
               SCOP domains d2y41b_ B: automated matches                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Iso_dh-2y41B01 B:2-344                                                                                                                                                                                                                                                                                                                                 -- Pfam domains (1)
           Pfam domains (2) --Iso_dh-2y41B02 B:2-344                                                                                                                                                                                                                                                                                                                                 -- Pfam domains (2)
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh...hhhhhhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhhhhhhh...eeeeeee....hhhhh..hhhhhh..eeeeeee..hhhhh....ee...eeeeeeeeehhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhh.........eee.....ee......hhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y41 B   0 SMKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFEAARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVLRHLAA 346
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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)

Thermus thermophilus [TaxId: 274] (5)

1a	d2y41a_	A:
1b	d2y41b_	B:

(no "CATH Domain" information available for 2Y41)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Iso_DH (49)

Family: Iso_dh (38)

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (11)

1a	Iso_dh-2y41B01	B:2-344
1b	Iso_dh-2y41B02	B:2-344

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (LEU3_THET8 | Q5SIY4)

molecular function
	GO:0003862	3-isopropylmalate dehydrogenase activity	Catalysis of the reaction: 3-carboxy-2-hydroxy-4-methylpentanoate + NAD+ = 3-carboxy-4-methyl-2-oxopentanoate + NADH + H+.
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0009082	branched-chain amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0009098	leucine biosynthetic process	The chemical reactions and pathways resulting in the formation of leucine, 2-amino-4-methylpentanoic acid.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:142 - Pro A:143	[ RasMol ]
		Glu B:142 - Pro B:143	[ RasMol ]

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	2y41
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1dpz	STUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD711
1dr0	STRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD708
1dr8	STRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD177
1g2u	THE STRUCTURE OF THE MUTANT, A172V, OF 3- ISOPROPYLMALATEDEHYDROGENASE FROM THERMUS THERMOPHILUS HB8 : ITSTHERMOSTABILITY AND STRUCTURE.
1gc8	THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE DEHYDROGENASE MUTATED AT 172TH FROM ALA TOPHE
1gc9	THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE DEHYDROGENASE MUTATED AT 172TH FROM ALA TOGLY
1hex	3-ISOPROPYLMALATE DEHYDROGENASE COMPLEXED WITH BETA-NICOTINAMIDE ADENINE DINUCLEOTIDE, OXIDIZED (NAD+)
1ipd	3-ISOPROPYLMALATE DEHYDROGENASE
1osi	STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE
1osj	STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE
1xaa	3-ISOPROPYLMALATE DEHYDROGENASE, LOW TEMPERATURE (100K) STRUCTURE
1xab	3-ISOPROPYLMALATE DEHYDROGENASE, LOW TEMPERATURE (150K) STRUCTURE
1xac	CHIMERA ISOPROPYLMALATE DEHYDROGENASE BETWEEN BACILLUS SUBTILIS (M) AND THERMUS THERMOPHILUS (T) FROM N-TERMINAL: 20% T MIDDLE 20% M RESIDUAL 60% T, MUTATED AT S82R. LOW TEMPERATURE (100K) STRUCTURE.
1xad	CHIMERA ISOPROPYLMALATE DEHYDROGENASE BETWEEN BACILLUS SUBTILIS (M) AND THERMUS THERMOPHILUS (T) FROM N-TERMINAL: 20% T MIDDLE 20% M RESIDUAL 60% T, MUTATED AT S82R. LOW TEMPERATURE (150K) STRUCTURE.
2y3z	STRUCTURE OF ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS
2y40	STRUCTURE OF ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS
2y42	STRUCTURE OF ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS - COMPLEX WITH NADH AND MN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (12, 12)

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