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(-) Description

Title :  STRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD177
 
Authors :  Z. Nurachman, S. Akanuma, T. Sato, T. Oshima, N. Tanaka
Date :  06 Jan 00  (Deposition) - 19 Jan 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dehydrogenase, Minor Groove, Paperclip Motion, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Nurachman, S. Akanuma, T. Sato, T. Oshima, N. Tanaka
Crystal Structures Of 3-Isopropylmalate Dehydrogenases With Mutations At The C-Terminus: Crystallographic Analyses Of Structure-Stability Relationships.
Protein Eng. V. 13 253 2000
PubMed-ID: 10810156  |  Reference-DOI: 10.1093/PROTEIN/13.4.253

(-) Compounds

Molecule 1 - 3-ISOPROPYLMALATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.85
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: LEUB
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: IPMDH, IMDH

 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 1DR8)

(-) Sites  (0, 0)

(no "Site" information available for 1DR8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DR8)

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DR8)

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DR8)

(-) 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:344
 aligned with LEU3_THET8 | Q5SIY4 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:344
                                    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 MKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFEAARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVLRHL 344
               SCOP domains d1dr8a_ A: 3-isopropylmalate dehydrogenase, IPMDH                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1dr8A00 A:1-344 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh...hhhhhhhhhhh..eeeee..hhhhh..hhhhhhhhhhhhhhhhh.eeeeeeeee....hhhhh..hhhhhh..eeeeeee..hhhhh.........eeeeeeeeehhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhh..hhhhh..eeee....ee.................hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ---------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dr8 A   1 MKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFELARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVGMGI 344
                                    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    


Chain B from PDB  Type:PROTEIN  Length:344
 aligned with LEU3_THET8 | Q5SIY4 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:344
                                    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 MKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFEAARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVLRHL 344
               SCOP domains d1dr8b_ B: 3-isopropylmalate dehydrogenase, IPMDH                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1dr8B00 B:1-344 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhh...hhhhhhhhhh...eeeee..hhhhh..hhhhhhhhhhhhhhhhh...eeeeeee....hhhhh..hhhhhh..eeeeeee..hhhhh....ee...eeeeeeeeehhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhh....hhhhh..eee.....ee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ---------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dr8 B   1 MKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFELARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVGMGI 344
                                    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 1DR8)

(-) 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:142 - Pro A:143   [ 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 1g2u 1gc8 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 PARTLY RESTORED THERMAL STABILITY MUTANT
1dr0 PARTLY RESTORED THERMAL STABILITY MUTANT
1osj MODIFIED 1OSJ AT THE C-TERMINUS