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(-) Description

Title :  3-ISOPROPYLMALATE DEHYDROGENASE FROM SHEWANELLA BENTHICA DB21 MT-2
 
Authors :  T. Nagae, N. Watanabe
Date :  13 Dec 11  (Deposition) - 29 Feb 12  (Release) - 12 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Decarboxylating Dehydrogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nagae, C. Kato, N. Watanabe
Structural Analysis Of 3-Isopropylmalate Dehydrogenase From The Obligate Piezophile Shewanella Benthica Db21Mt-2 And Th Nonpiezophile Shewanella Oneidensis Mr-1
Acta Crystallogr. , Sect. F V. 68 265 2012
PubMed-ID: 22442218  |  Reference-DOI: 10.1107/S1744309112001443

(-) Compounds

Molecule 1 - 3-ISOPROPYLMALATE DEHYDROGENASE
    Chains: A, B
    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
    Organism Scientific: SHEWANELLA BENTHICA
    Organism Taxid: 43661
    Strain: DB21 MT-2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2IPM2Ligand/Ion3-ISOPROPYLMALIC ACID
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:97 , ARG A:136 , TYR A:143 , ASP A:249 , MG A:402 , HOH A:559 , HOH A:634 , HOH A:771 , LYS B:193 , ASN B:195 , ASP B:225 , HOH B:741BINDING SITE FOR RESIDUE IPM A 401
2AC2SOFTWAREASP A:249 , IPM A:401 , HOH A:682 , ASP B:225 , HOH B:741BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWAREGLY A:141 , ILE A:142 , LEU A:246 , HOH A:747BINDING SITE FOR RESIDUE CL A 403
4AC4SOFTWARELYS A:193 , ASN A:195 , ASP A:225 , HOH A:551 , ARG B:97 , ARG B:107 , ARG B:136 , TYR B:143 , ASP B:249 , MG B:402 , HOH B:506 , HOH B:618 , HOH B:647 , HOH B:795BINDING SITE FOR RESIDUE IPM B 401
5AC5SOFTWAREASP A:225 , HOH A:551 , ASP B:249 , IPM B:401 , HOH B:506BINDING SITE FOR RESIDUE MG B 402
6AC6SOFTWAREGLY B:141 , ILE B:142 , ASN B:245 , LEU B:246 , HOH B:803BINDING SITE FOR RESIDUE CL B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:146 -Pro A:147
2Lys B:146 -Pro B:147

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VMK)

(-) Exons   (0, 0)

(no "Exon" information available for 3VMK)

(-) Sequences/Alignments

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:369
 aligned with D2YZL2_9GAMM | D2YZL2 from UniProtKB/TrEMBL  Length:364

    Alignment length:369
                                  1                                                                                                                                                                                                                                                                                                                                                                          
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354         
         D2YZL2_9GAMM     - ------MSYQIAVLAGDGIGPEVMAEARKVLAAVEKRFDLSIEYSEYDVGGAAIDNHGCPLPEATLKGCEAADAVLFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHPGLEHMSPLRSDISEKGFDILCVRELTGGIYFGKPKGRQGEGENEEAFDTMRYSRKEIRRIAKIAFESAQGRRKKVTSVDKANVLACSVLWREVVEEVAKDYPDVELEHIYIDNATMQLLRRPNEFDVMLCSNLFGDIVSDEIAMLTGSMGLLASISMNSQGFGMYEPAGGSAPDIAGQGIANPVAQILSAALLLRHSLKLEDAALAIEAAVSKALSDGYLTCELLPASERSQAKSTSQMGDYIAQAIAEG 363
               SCOP domains d3vmka_ A: 3-isopropylmalate dehydrogenase, IPMDH                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeee..hhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhh...hhhhhhhhhh..eeeeee..hhhhh......hhhhhhhhhhhhhh...eeeeeee....hhhhh..hhhhhh...eeeeeee...........eee.hhhh.eeeeeeeeehhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeee...............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vmk A  -5 HHHHHGSSYQIAVLAGDGIGPEVMAEARKVLAAVEKRFDLSIEYSEYDVGGAAIDNHGCPLPEATLKGCEAADAVLFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHPGLEHMSPLRSDISEKGFDILCVRELTGGIYFGKPKGRQGEGENEEAFDTMRYSRKEIRRIAKIAFESAQGRRKKVTSVDKANVLACSVLWREVVEEVAKDYPDVELEHIYIDNATMQLLRRPNEFDVMLCSNLFGDIVSDEIAMLTGSMGLLASISMNSQGFGMYEPAGGSAPDIAGQGIANPVAQILSAALLLRHSLKLEDAALAIEAAVSKALSDGYLTCELLPASERSQAKSTSQMGDYIAQAIAEG 363
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354         


Chain B from PDB  Type:PROTEIN  Length:368
 aligned with D2YZL2_9GAMM | D2YZL2 from UniProtKB/TrEMBL  Length:364

    Alignment length:368
                                 1                                                                                                                                                                                                                                                                                                                                                                          
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355        
         D2YZL2_9GAMM     - -----MSYQIAVLAGDGIGPEVMAEARKVLAAVEKRFDLSIEYSEYDVGGAAIDNHGCPLPEATLKGCEAADAVLFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHPGLEHMSPLRSDISEKGFDILCVRELTGGIYFGKPKGRQGEGENEEAFDTMRYSRKEIRRIAKIAFESAQGRRKKVTSVDKANVLACSVLWREVVEEVAKDYPDVELEHIYIDNATMQLLRRPNEFDVMLCSNLFGDIVSDEIAMLTGSMGLLASISMNSQGFGMYEPAGGSAPDIAGQGIANPVAQILSAALLLRHSLKLEDAALAIEAAVSKALSDGYLTCELLPASERSQAKSTSQMGDYIAQAIAEG 363
               SCOP domains d3vmkb_ B: 3-isopropylmalate dehydrogenase, IPMDH                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh...hhhhhhhhhh..eeeeee..hhhhh..hhhhhhhhhhhhhhhhhh...eeeeeee....hhhhh..hhhhhh...eeeeeee...........eee.hhhh.eeeeeeeeehhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeee...............hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vmk B  -4 HHHHGSSYQIAVLAGDGIGPEVMAEARKVLAAVEKRFDLSIEYSEYDVGGAAIDNHGCPLPEATLKGCEAADAVLFGSVGGPKWEHLPPNDQPERGALLPLRGHFELFCNMRPAKLHPGLEHMSPLRSDISEKGFDILCVRELTGGIYFGKPKGRQGEGENEEAFDTMRYSRKEIRRIAKIAFESAQGRRKKVTSVDKANVLACSVLWREVVEEVAKDYPDVELEHIYIDNATMQLLRRPNEFDVMLCSNLFGDIVSDEIAMLTGSMGLLASISMNSQGFGMYEPAGGSAPDIAGQGIANPVAQILSAALLLRHSLKLEDAALAIEAAVSKALSDGYLTCELLPASERSQAKSTSQMGDYIAQAIAEG 363
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VMK)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

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 Related Entries

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        D2YZL2_9GAMM | D2YZL2: 3vml

(-) Related Entries Specified in the PDB File

3vmj 3vml