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(-) Description

Title :  CRYSTAL STRUCTURE OF ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE FROM SALMONELLA ENTERICASE
 
Authors :  Y. Kim, M. Zhou, S. Peterson, W. F. Anderson, A. Joachimiak
Date :  22 Jun 09  (Deposition) - 30 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.52
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Alpha-Beta Structure, Isomerase, Isoprene Biosynthesis, Magnesium, Manganese, Metal-Binding, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, M. Zhou, S. Peterson, W. F. Anderson, A. Joachimiak
Crystal Structure Of Isopentenyl-Diphosphate Delta-Isomeras From Salmonella Entericase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE
    Chains: A
    EC Number: 5.3.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: IDI
    Ipp: DMAPP ISOMERASE
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2
    Synonym: IPP ISOMERASE, ISOPENTENYL PYROPHOSPHATE ISOMERASE,

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:151
 aligned with IDI_SALTY | Q8ZM82 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:151
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
            IDI_SALTY    31 LHLAFSCWLFNEDGQLLVTRRSLSKKAWPGVWTNSVCGHPQQGETTEEAIIRRCRFELGVEITDLTPVYPHFSYRATDPNGIVENEVCPVFAARATSVLQVNSEEVMDYQWSEFKSVWKSLLATPWAFSPWMVMQASDEQARERLLNYCQR 181
               SCOP domains d3hyqa_ A: Isopentenyl diphosphate isomerase                                                                                                            SCOP domains
               CATH domains 3hyqA00 A:31-181 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....eeeeee..........ee..eee......hhhhhhhhhhhhhhh..eeeeeeee...eeeee.....eeeee..eeeeee..........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hyq A  31 LHLAFSCWLFNEDGQLLVTRRSLSKKAWPGVWTNSVCGHPQQGETTEEAIIRRCRFELGVEITDLTPVYPHFSYRATDPNGIVENEVCPVFAARATSVLQVNSEEVmDYQWSEFKSVWKSLLATPWAFSPWmVmQASDEQARERLLNYCQR 181
                                    40        50        60        70        80        90       100       110       120       130      |140       150       160 | |   170       180 
                                                                                                                                    137-MSE                  162-MSE               
                                                                                                                                                               164-MSE
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (IDI_SALTY | Q8ZM82)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0004452    isopentenyl-diphosphate delta-isomerase activity    Catalysis of the reaction: isopentenyl diphosphate = dimethylallyl diphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0050992    dimethylallyl diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of dimethylallyl diphosphate.
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
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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