Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS - APO ENZYME
 
Authors :  E. Graczer, A. Merlin, R. K. Singh, K. Manikandan, P. Zavodsky, M. S. Wei
Date :  04 Jan 11  (Deposition) - 19 Jan 11  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase, Leub, Leucine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Graczer, A. Merli, R. K. Singh, M. Karuppasamy, P. Zavodszky, M. S. Weiss, M. Vas
Atomic Level Description Of The Domain Closure In A Dimeric Enzyme: Thermus Thermophilus 3-Isopropylmalate Dehydrogenase.
Mol. Biosyst. V. 7 1646 2011
PubMed-ID: 21387033  |  Reference-DOI: 10.1039/C0MB00346H
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-ISOPROPYLMALATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.85
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET21C
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Other Details: ADDITIONAL AMINO ACIDS- N-TERMINAL MAS. C- TERMINAL AAALEHHHHHH
    Synonym: ISOPROPYLMALATE DEHYDROGENASE, 3-IPM-DH, BETA-IPM DEHYDROGENASE, IMDH, IPMDH

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
12PE3Ligand/IonNONAETHYLENE GLYCOL
2GOL3Ligand/IonGLYCEROL
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
12PE6Ligand/IonNONAETHYLENE GLYCOL
2GOL6Ligand/IonGLYCEROL
3TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:104 , ASP A:217 , ASP A:241 , ASP A:245 , HOH A:2115 , HOH A:2142 , HOH A:2143 , HOH A:2198BINDING SITE FOR RESIDUE TRS A1351
2AC2SOFTWAREGLU A:171 , ALA A:172 , LYS A:175 , ASP A:278 , ALA A:280 , HIS A:300 , ALA A:301 , PHE A:302 , GLY A:303 , HOH A:2200BINDING SITE FOR RESIDUE 2PE A1352
3AC3SOFTWAREARG A:94 , ASN A:102 , ARG A:104 , ARG A:132 , PHE A:140 , VAL A:188 , SER A:259 , GLU A:270 , GOL A:1357 , HOH A:2142BINDING SITE FOR RESIDUE 2PE A1353
4AC4SOFTWAREVAL A:72 , GLY A:73 , GLY A:74 , LEU A:254 , HIS A:273 , GLY A:274 , SER A:275 , ALA A:276 , PRO A:277 , ALA A:285 , ASN A:286 , GOL A:1357 , HOH A:2199 , HOH A:2201BINDING SITE FOR RESIDUE 2PE A1354
5AC5SOFTWARELYS A:76 , GLY A:303 , VAL A:305 , HOH A:2200BINDING SITE FOR RESIDUE GOL A1355
6AC6SOFTWAREGLU A:212 , GLN A:214 , ARG A:229BINDING SITE FOR RESIDUE GOL A1356
7AC7SOFTWARESER A:71 , VAL A:72 , GLU A:270 , PRO A:271 , VAL A:272 , HIS A:273 , GLY A:274 , 2PE A:1353 , 2PE A:1354 , HOH A:2039 , HOH A:2201BINDING SITE FOR RESIDUE GOL A1357

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y3Z)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:142 -Pro A:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y3Z)

(-) PROSITE Motifs  (1, 1)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2Y3Z)

(-) Sequences/Alignments

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:351
 aligned with LEU3_THET8 | Q5SIY4 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:351
                             1                                                                                                                                                                                                                                                                                                                                                     345     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339     |   - 
           LEU3_THET8     - -MKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFEAARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVLRHLA-----   -
               SCOP domains d2y3za_ A: automated matches                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Iso_dh-2y3zA01 A:2-344                                                                                                                                                                                                                                                                                                                                 ------ Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhh...hhhhhhhhhhh.eeee....hhhhh..hhhhhhhhhhhhhhhhh.eeeeeeeee....hhhhh..hhhhhh..eeeeeee...........ee....ee.....hhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhh...hhhh.eeeeee....eeee....hhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y3z A   0 SMKVAVLPGDGIGPEVTEAALKVLRALDEAEGLGLAYEVFPFGGAAIDAFGEPFPEPTRKGVEEAEAVLLGSVGGPKWDGLPRKIRPETGLLSLRKSQDLFANLRPAKVFPGLERLSPLKEEIARGVDVLIVRELTGGIYFGEPRGMSEAEAWNTERYSKPEVERVARVAFEAARKRRKHVVSVDKANVLEVGEFWRKTVEEVGRGYPDVALEHQYVDAMAMHLVRSPARFDVVVTGNIFGDILSDLASVLPGSLGLLPSASLGRGTPVFEPVHGSAPDIAGKGIANPTAAILSAAMMLEHAFGLVELARKVEDAVAKALLETPPPDLGGSAGTEAFTATVLRHLAAAALE 350
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y3Z)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Iso_DH (49)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    2PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:142 - Pro A:143   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2y3z
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LEU3_THET8 | Q5SIY4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.1.1.85
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  LEU3_THET8 | Q5SIY4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LEU3_THET8 | Q5SIY4: 1dpz 1dr0 1dr8 1g2u 1gc8 1gc9 1hex 1idm 1ipd 1osi 1osj 1xaa 1xab 1xac 1xad 2y40 2y41 2y42 2ztw 4f7i 4wuo

(-) Related Entries Specified in the PDB File

1dpz STUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD711
1dr0 STRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD708
1dr8 STRUCTURE OF MODIFIED 3-ISOPROPYLMALATE DEHYDROGENASE AT THE C-TERMINUS, HD177
1g2u THE STRUCTURE OF THE MUTANT, A172V, OF 3- ISOPROPYLMALATEDEHYDROGENASE FROM THERMUS THERMOPHILUS HB8 : ITSTHERMOSTABILITY AND STRUCTURE.
1gc8 THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE DEHYDROGENASE MUTATED AT 172TH FROM ALA TOPHE
1gc9 THE CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS 3-ISOPROPYLMALATE DEHYDROGENASE MUTATED AT 172TH FROM ALA TOGLY
1hex 3-ISOPROPYLMALATE DEHYDROGENASE COMPLEXED WITH BETA-NICOTINAMIDE ADENINE DINUCLEOTIDE, OXIDIZED(NAD+)
1ipd 3-ISOPROPYLMALATE DEHYDROGENASE
1osi STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE
1osj STRUCTURE OF 3-ISOPROPYLMALATE DEHYDROGENASE
1xaa 3-ISOPROPYLMALATE DEHYDROGENASE, LOW TEMPERATURE (100K) STRUCTURE
1xab 3-ISOPROPYLMALATE DEHYDROGENASE, LOW TEMPERATURE (150K) STRUCTURE
1xac CHIMERA ISOPROPYLMALATE DEHYDROGENASE BETWEEN BACILLUS SUBTILIS (M) AND THERMUS THERMOPHILUS (T) FROM N-TERMINAL: 20% T MIDDLE 20% M RESIDUAL 60% T, MUTATED AT S82R. LOW TEMPERATURE (100K) STRUCTURE.
1xad CHIMERA ISOPROPYLMALATE DEHYDROGENASE BETWEEN BACILLUS SUBTILIS (M) AND THERMUS THERMOPHILUS (T) FROM N-TERMINAL: 20% T MIDDLE 20% M RESIDUAL 60% T, MUTATED AT S82R. LOW TEMPERATURE (150K) STRUCTURE.
2y40 STRUCTURE OF ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS
2y41 STRUCTURE OF ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS
2y42 STRUCTURE OF ISOPROPYLMALATE DEHYDROGENASE FROM THERMUS THERMOPHILUS - COMPLEX WITH NADH AND MN