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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE DEHYDROGENASE MUTATED AT 172TH FROM ALA TO PHE
 
Authors :  C. Qu, S. Akanuma, N. Tanaka, H. Moriyama, T. Oshima
Date :  27 Jul 00  (Deposition) - 27 Sep 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ipmdh, Imdh, Thermostability, Dehydrogenation, Decarboxylation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Qu, S. Akanuma, N. Tanaka, H. Moriyama, T. Oshima
Design, X-Ray Crystallography, Molecular Modelling And Thermal Stability Studies Of Mutant Enzymes At Site 172 Of 3-Isopropylmalate Dehydrogenase From Thermus Thermophilus.
Acta Crystallogr. , Sect. D V. 57 225 2001
PubMed-ID: 11173468  |  Reference-DOI: 10.1107/S0907444900017388

(-) Compounds

Molecule 1 - 3-ISOPROPYLMALATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.85
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: JA221
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LEUB
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1GC8)

(-) Sites  (0, 0)

(no "Site" information available for 1GC8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GC8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:1142 -Pro A:1143
2Glu B:142 -Pro B:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GC8)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDH_IMDHPS00470 Isocitrate and isopropylmalate dehydrogenases signature.LEU3_THET8237-256
 		  2A:1237-1256
B:237-256

(-) Exons   (0, 0)

(no "Exon" information available for 1GC8)

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

    Alignment length:345
                                    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     
          LEU3_THET8      1 MKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFEAARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVLRHLA  345
               SCOP domains d1gc8a_ A: 3-isopropylmalate dehydrogenase, IPMDH                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1gc8A00 A:1001-1345 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh...hhhhhhhhhhh.eeeeee..hhhhhh.hhhhhhhhhhhhhhhhh.eeeeeeeee...hhhhhh..hhhhhh..eeeeeee...........ee...eeeeeeeeehhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhh....hhhh.eeeeee....eeee....hhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ----------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1gc8 A 1001 MKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFEFARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVLRHLA 1345
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340     


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

    Alignment length:345
                                    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     
          LEU3_THET8      1 MKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFEAARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVLRHLA  345
               SCOP domains d1gc8b_ B: 3-isopropylmalate dehydrogenase, IPMDH                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1gc8B00 B:1-345 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh...hhhhhhhhhhh.eeeeee..hhhhhh.hhhhhhhhhhhhhhhhhheeeeeeeee....hhhhh..hhhhhh..eeeeeee...........ee...eeeeeeeeehhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhh..........eeee....ee.................hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ----------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1gc8 B    1 MKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFEFARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVLRHLA  345
                                    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
   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 1GC8)

(-) Gene Ontology  (12, 12)

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.

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  Cis Peptide Bonds
    Glu A:1142 - Pro A:1143   [ RasMol ]  
    Glu B:142 - Pro B:143   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        LEU3_THET8 | Q5SIY4: 1dpz 1dr0 1dr8 1g2u 1gc9 1hex 1idm 1ipd 1osi 1osj 1xaa 1xab 1xac 1xad 2y3z 2y40 2y41 2y42 2ztw 4f7i 4wuo

(-) Related Entries Specified in the PDB File

1dpz 1DPZ CONTAINS THE C-TERMINAL MUTANT OF A172L.
1dr0 1DR0 CONTAINS THE C-TERMINAL MUTANT OF A172L.
1dr8 1DR8 CONTAINS THE C-TERMINAL MUTANT OF A172L.
1gc9 1GC9 CONTAINS A172G.
1ipd 1IPD CONTAINS THE WILD TYPE ENZYME PRODUCED BY THERMUS THERMOPHILUS.
1osj 1OSJ CONTAINS A172L.