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Title :   CHIMERA 3-ISOPROPYLMALATE DEHYDROGENASE BETWEEN SHEWANELLA ONEIDENSIS MR-1 (O) AND SHEWANELLA BENTHICA DB21 MT-2 (M) FROM N-TERMINAL: 20% O MIDDLE 70% M RESIDUAL 10% O

Authors :   T. Nagae, N. Watanabe

Date :   13 Dec 11 (Deposition) - 26 Dec 12 (Release) - 26 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.56

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

Keywords :   Oxidoreductase, Decarboxylating Dehydrogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Hamajima, T. Nagae, N. Watanabe, C. Kato
Structure Analysis Of Chimeric 3-Isopropylmalate Dehydrogenase Between The Obligate Piezophile Shewanella Benthica Db21Mt-2 And The Nonpiezophile Shewanella Oneidensis Mr-1
To Be Published
PubMed: search

Molecule 1 - 3-ISOPROPYLMALATE DEHYDROGENASE
	Chains	:	A
	EC Number	:	1.1.1.85
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE80
	Expression System Strain	:	BL21 CODONPLUS(DE3) RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LEUB, SO_4235
	Organism Scientific	:	SHEWANELLA ONEIDENSIS, SHEWANELLA BENTHICA, SHEWANELLA ONEIDENSIS
	Organism Taxid	:	211586, 43661, 211586
	Other Details	:	CHIMERA PROTEIN OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM SHEWANELLA ONEIDENSIS MR-1 (UNP Q8E9N3 RESIDUES 2-68), 3- ISOPROPYLMALATE DEHYDROGENASE FROM SHEWANELLA BENTHICA DB21 MT-2 (UNP D2YZL2 RESIDUES 69-328), AND 3-ISOPROPYLMALATE DEHYDROGENASE FROM SHEWANELLA ONEIDENSIS MR-1 (UNP Q8E9N3 RESIDUES 329-364)
	Strain	:	MR-1, DB21 MT-2, MR-1
	Synonym	:	3-IPM-DH, BETA-IPM DEHYDROGENASE, IMDH

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	IPM	1	Ligand/Ion	3-ISOPROPYLMALIC ACID
3	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IPM	2	Ligand/Ion	3-ISOPROPYLMALIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:97 , ARG A:107 , ARG A:136 , TYR A:143 , LYS A:193 , ASN A:195 , ASP A:225 , ASP A:249 , MG A:402 , HOH A:518 , HOH A:526 , HOH A:557 , HOH A:952 , HOH A:963	BINDING SITE FOR RESIDUE IPM A 401
2	AC2	SOFTWARE	ASP A:225 , ASP A:249 , IPM A:401 , HOH A:952 , HOH A:963	BINDING SITE FOR RESIDUE MG A 402
3	AC3	SOFTWARE	GLY A:141 , ILE A:142 , ASN A:245 , LEU A:246 , HOH A:964	BINDING SITE FOR RESIDUE CL A 403

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

Asymmetric Unit

No.	Residues
1	Lys A:146	-	Pro A:147

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IDH_IMDH	PS00470	Isocitrate and isopropylmalate dehydrogenases signature.	LEU3_SHEON	245-264	1	A:245-264

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.	LEU3_SHEON	245-264	2	A:245-264

(no "Exon" information available for 3VML)

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:363
 aligned with D2YZL2_9GAMM | D2YZL2 from UniProtKB/TrEMBL  Length:364

    Alignment length:363
                                    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   
         D2YZL2_9GAMM     1 MSYQIAVLAGDGIGPEVMAEARKVLAAVEKRFDLSIEYSEYDVGGAAIDNHGCPLPEATLKGCEAADAVLFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHPGLEHMSPLRSDISEKGFDILCVRELTGGIYFGKPKGRQGEGENEEAFDTMRYSRKEIRRIAKIAFESAQGRRKKVTSVDKANVLACSVLWREVVEEVAKDYPDVELEHIYIDNATMQLLRRPNEFDVMLCSNLFGDIVSDEIAMLTGSMGLLASISMNSQGFGMYEPAGGSAPDIAGQGIANPVAQILSAALLLRHSLKLEDAALAIEAAVSKALSDGYLTCELLPASERSQAKSTSQMGDYIAQAIAEG 363
               SCOP domains d3vmla_ A: automated matches                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh...hhhhhhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhhhhhhhh...eeeeeee....hhhhh..hhhhhh...eeeeeee..hhhhh....eee.hhhhheee.....hhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeee....hhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhh...hhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vml A   1 SSYQIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYTEYDVGGIAIDNHGCPLPEATLKGCEAADAVLFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHPGLEHMSPLRSDISEKGFDILCVRELTGGIYFGKPKGRQGEGENEEAFDTMRYSRKEIRRIAKIAFESAQGRRKKVTSVDKANVLACSVLWREVVEEVAKDYPDVELEHIYIDNATMQLLRRPNEFDVMLCSNLFGDIVSDEIAMLTGSMGLLASISMNSQGFGMYEPAGGSAPDIAGQGIANPVAQILSAALLLRHSLKLEDAALAIEAAVSKALNSGYLTGELLSSDQRHKAKTTVQMGDFIADAVKAG 363
                                    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

Chain A from PDB  Type:PROTEIN  Length:363
 aligned with LEU3_SHEON | Q8E9N3 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:363
                                    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   
           LEU3_SHEON     1 MSYQIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYTEYDVGGIAIDNHGCPLPEATLKGCEAADAILFGSVGGPKWEKLPPNEQPERGALLPLRGHFELFCNLRPAKLHDGLEHMSPLRSDISARGFDVLCVRELTGGIYFGKPKGRQGEGESEEAFDTMRYSRREISRIARIAFEAARGRRKKVTSVDKANVLACSVLWRQVVEEVAVDFPDVELEHIYIDNATMQLLRRPDEFDVMLCSNLFGDILSDEIAMLTGSMGLLSSASMNSTGFGLFEPAGGSAPDIAGKGIANPIAQILSAALMLRHSLKQEEAASAIERAVTKALNSGYLTGELLSSDQRHKAKTTVQMGDFIADAVKAG 363
               SCOP domains d3vmla_ A: automated matches                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh...hhhhhhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhhhhhhhh...eeeeeee....hhhhh..hhhhhh...eeeeeee..hhhhh....eee.hhhhheee.....hhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeee....hhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhh...hhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vml A   1 SSYQIAVLAGDGIGPEVMAEARKVLKAVEARFGLNIEYTEYDVGGIAIDNHGCPLPEATLKGCEAADAVLFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHPGLEHMSPLRSDISEKGFDILCVRELTGGIYFGKPKGRQGEGENEEAFDTMRYSRKEIRRIAKIAFESAQGRRKKVTSVDKANVLACSVLWREVVEEVAKDYPDVELEHIYIDNATMQLLRRPNEFDVMLCSNLFGDIVSDEIAMLTGSMGLLASISMNSQGFGMYEPAGGSAPDIAGQGIANPVAQILSAALLLRHSLKLEDAALAIEAAVSKALNSGYLTGELLSSDQRHKAKTTVQMGDFIADAVKAG 363
                                    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

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 "CATH Domain" information available for 3VML)

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

Asymmetric Unit(hide GO term definitions)

Chain A (LEU3_SHEON | Q8E9N3)

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: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.

Chain A (D2YZL2_9GAMM | D2YZL2)

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: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 Unit
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	Cis Peptide Bonds
		Lys A:146 - Pro A:147	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	LEU3_SHEON \| Q8E9N3
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	1.1.1.85
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UniProtKB/Swiss-Prot
	LEU3_SHEON \| Q8E9N3	:	3vkz 3vl2 3vl3 3vl4 3vl6 3vl7 3vmj 3wzv 3wzw 3wzx 3wzy
UniProtKB/TrEMBL
	D2YZL2_9GAMM \| D2YZL2	:	3vmk

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (11, 22)

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