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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE ISOPROPYLAMLATE DEHYDROGENASE FROM CAMPYLOBACTER JEJUNI
 
Authors :  K. L. Tkaczuk, M. Chruszcz, B. J. Blus, O. Onopriyenko, S. Grimshaw, A. S W. F. Anderson, W. Minor, Center For Structural Genomics Of Infe Diseases (Csgid)
Date :  28 Oct 11  (Deposition) - 09 Nov 11  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Putative Isopropylamlate Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. L. Tkaczuk, M. Chruszcz, B. J. Blus, O. Onopriyenko, S. Grimshaw, A. Savchenko, W. F. Anderson, W. Minor, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Putative Isopropylamlate Dehydrogenase From Campylobacter Jejuni
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-ISOPROPYLMALATE DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.85
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LEUB, CJ1718C
    Organism Scientific: CAMPYLOBACTER JEJUNI
    Organism Taxid: 197
    Synonym: 3-IPM-DH, BETA-IPM DEHYDROGENASE, IMDH

 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, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 28)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MSE16Mod. Amino AcidSELENOMETHIONINE
3SO48Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:291 , HOH A:408BINDING SITE FOR RESIDUE EDO A 359
2AC2SOFTWAREPRO A:109 , CYS A:110 , LYS A:111 , TYR A:113 , ASN A:255 , LEU A:260 , LEU A:261BINDING SITE FOR RESIDUE EDO A 360
3AC3SOFTWAREARG A:98 , ARG A:137 , ASP A:245 , SO4 A:364 , HOH A:424 , HOH A:442BINDING SITE FOR RESIDUE SO4 A 361
4AC4SOFTWAREARG A:108 , ASP A:249 , ALA A:277BINDING SITE FOR RESIDUE SO4 A 362
5AC5SOFTWAREILE A:85 , ARG A:88BINDING SITE FOR RESIDUE SO4 A 363
6AC6SOFTWAREARG A:98 , ASN A:106 , ARG A:108 , SER A:263 , GLU A:275 , ALA A:277 , SO4 A:361 , HOH A:442BINDING SITE FOR RESIDUE SO4 A 364

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UDO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDH_IMDHPS00470 Isocitrate and isopropylmalate dehydrogenases signature.LEU3_CAMJE241-260  1A:241-260
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDH_IMDHPS00470 Isocitrate and isopropylmalate dehydrogenases signature.LEU3_CAMJE241-260  2A:241-260

(-) Exons   (0, 0)

(no "Exon" information available for 3UDO)

(-) 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:355
 aligned with LEU3_CAMJE | Q9PLW0 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:355
                                    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_CAMJE     1 MKTYKVAVLAGDGIGPLVMKEALKILTFIAQKYNFSFEFNEAKIGGASIDAYGVALSDETLKLCEQSDAILFGSVGGPKWDNLPIDQRPERASLLPLRKHFNLFANLRPCKIYESLTHASPLKNEIIQKGVDILCVRELTGGIYFGKQDLGKESAYDTEIYTKKEIERIARIAFESARIRKKKVHLIDKANVLASSILWREVVANVAKDYQDINLEYMYVDNAAMQIVKNPSIFDVMLCSNLFGDILSDELAAINGSLGLLSSASLNDKGFGLYEPAGGSAPDIAHLNIANPIAQILSAALMLKYSFKEEQAAQDIENAISLALAQGKMTKDLNAKSYLNTDEMGDCILEILKEN 355
               SCOP domains d3udoa_ A: automated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhh...hhhhhhhhhh..eeeeee..hhhhh..hhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhh..hhhhhhh..eeeeeee..hhhhh...ee....ee.....hhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeee....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3udo A   1 mKTYKVAVLAGDGIGPLVmKEALKILTFIAQKYNFSFELNEAKIGGASIDAYGVALSDETLKLCEQSDAILFGSVGGPKWDNLPIDQRPERASLLPLRKHFNLFANLRPCKIYESLTHASPLKNEIIQKGVDILCVRELTGGIYFGKQDLGKESAYDTEIYTKKEIERIARIAFESARIRKKKVHLIDKANVLASSILWREVVANVAKDYQDINLEYmYVDNAAmQIVKNPSIFDVmLCSNLFGDILSDELAAINGSLGLLSSASLNDKGFGLYEPAGGSAPDIAHLNIANPIAQILSAALmLKYSFKEEQAAQDIENAISLALAQGKmTKDLNAKSYLNTDEmGDCILEILKEN 355
                            |       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     
                            |                19-MSE                                                                                                                                                                                                218-MSE  |         237-MSE                                                          302-MSE                    329-MSE        344-MSE       
                            1-MSE                                                                                                                                                                                                                         225-MSE
   Legend:   → Mismatch (orange background)
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    → 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 3UDO)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (LEU3_CAMJE | Q9PLW0)
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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