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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THIOBACILLUS FERROOXIDANS WITH 3-ISOPROPYLMALATE
 
Authors :  K. Imada, K. Inagaki, H. Matsunami, H. Kawaguchi, H. Tanaka, N. Tanaka, K. Namba
Date :  09 Dec 97  (Deposition) - 17 Jun 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Decarboxylating Dehydrogenase, Leucine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Imada, K. Inagaki, H. Matsunami, H. Kawaguchi, H. Tanaka, N. Tanaka, K. Namba
Structure Of 3-Isopropylmalate Dehydrogenase In Complex With 3-Isopropylmalate At 2. 0 A Resolution: The Role Of Glu88 In The Unique Substrate-Recognition Mechanism.
Structure V. 6 971 1998
PubMed-ID: 9739088  |  Reference-DOI: 10.1016/S0969-2126(98)00099-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-ISOPROPYLMALATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.85
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKKLEUB1
    Expression System Strain: JA221
    Expression System Taxid: 562
    Gene: LEUB
    Organism Scientific: ACIDITHIOBACILLUS FERROOXIDANS
    Organism Taxid: 920
    Strain: AP19-3
    Synonym: IPMDH, IMDH

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1IPM2Ligand/Ion3-ISOPROPYLMALIC ACID
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:246 , IPM A:401 , HOH A:562 , HOH A:602 , ASP B:222BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREASP A:222 , HOH A:532 , ASP B:246 , IPM B:402 , HOH B:419BINDING SITE FOR RESIDUE MG A 502
3AC3SOFTWAREGLU A:88 , ARG A:95 , ARG A:105 , ARG A:133 , TYR A:140 , ASP A:246 , MG A:501 , HOH A:553 , HOH A:693 , LYS B:190 , VAL B:193 , ASP B:222BINDING SITE FOR RESIDUE IPM A 401
4AC4SOFTWARELYS A:190 , VAL A:193 , ASP A:222 , MG A:502 , ARG B:95 , ARG B:105 , ARG B:133 , TYR B:140 , ASP B:246 , HOH B:428 , HOH B:441BINDING SITE FOR RESIDUE IPM B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1A05)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:143 -Pro A:144
2Gln B:143 -Pro B:144

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A05)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDH_IMDHPS00470 Isocitrate and isopropylmalate dehydrogenases signature.LEU3_ACIFR242-261
 		  2A:242-261
B:242-261

(-) Exons   (0, 0)

(no "Exon" information available for 1A05)

(-) 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:357
 aligned with LEU3_ACIFR | Q56268 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:357
                                    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       
           LEU3_ACIFR     1 MKKIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLAMAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRPELVRDVDILVVRELTGDIYFGQPRGLEVIDGKRRGFNTMVYDEDEIRRIAHVAFRAAQGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVLLTGNMFGDILSDEASQLTGSIGMLPSASLGEGRAMYEPIHGSAPDIAGQDKANPLATILSVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNALNLK 357
               SCOP domains d1a05a_ A: 3-isopropylmalate dehydrogenase, IPMDH                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1a05A00 A:1-357 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhh....hhhhhhhhhh..eeeeee..............hhhhhhhhhhh....eeeeeee...................eeeeeee..........eeeeee..eeeeeeeeeeehhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhh......eeee.hhhhhhhhhhhhhhh......eeeee....eeeee...............hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh................hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a05 A   1 MKKIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLAMAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRPELVRDVDILVVRELTGDIYFGQPRGLEVIDGKRRGFNTMVYDEDEIRRIAHVAFRAAQGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVLLTGNMFGDILSDEASQLTGSIGMLPSASLGEGRAMYEPIHGSAPDIAGQDKANPLATILSVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNALNLK 357
                                    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       


Chain B from PDB  Type:PROTEIN  Length:357
 aligned with LEU3_ACIFR | Q56268 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:357
                                    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       
           LEU3_ACIFR     1 MKKIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLAMAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRPELVRDVDILVVRELTGDIYFGQPRGLEVIDGKRRGFNTMVYDEDEIRRIAHVAFRAAQGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVLLTGNMFGDILSDEASQLTGSIGMLPSASLGEGRAMYEPIHGSAPDIAGQDKANPLATILSVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNALNLK 357
               SCOP domains d1a05b_ B: 3-isopropylmalate dehydrogenase, IPMDH                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1a05B00 B:1-357 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhh....hhhhhhhhhh..eeeeee..............hhhhhhhhhhh....eeeeeee...................eeeeeee..........eeeeee..eeeeeeeeeeehhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhh......eeee.hhhhhhhhhhhhhhh......eeeee....eeeee...............hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh................hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a05 B   1 MKKIAIFAGDGIGPEIVAAARQVLDAVDQAAHLGLRCTEGLVGGAALDASDDPLPAASLQLAMAADAVILGAVGGPRWDAYPPAKRPEQGLLRLRKGLDLYANLRPAQIFPQLLDASPLRPELVRDVDILVVRELTGDIYFGQPRGLEVIDGKRRGFNTMVYDEDEIRRIAHVAFRAAQGRRKQLCSVDKANVLETTRLWREVVTEVARDYPDVRLSHMYVDNAAMQLIRAPAQFDVLLTGNMFGDILSDEASQLTGSIGMLPSASLGEGRAMYEPIHGSAPDIAGQDKANPLATILSVAMMLRHSLNAEPWAQRVEAAVQRVLDQGLRTADIAAPGTPVIGTKAMGAAVVNALNLK 357
                                    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
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A05)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LEU3_ACIFR | Q56268)
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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