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(-) Description

Title :  E.COLI IPP ISOMERASE IN COMPLEX WITH DIPHOSPHATE
 
Authors :  J. Wouters, V. Durisotti, Y. Oudjama, V. Stalon, L. Droogmans
Date :  27 Jun 03  (Deposition) - 06 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ipp Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Wouters, V. Durisotti, Y. Oudjama, V. Stalon, L. Droogmans
E. Coli Isopentenyl Diphosphate: Dimethylallyl Diphosphate Isomerase In Complex With Diphosphate
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE
    Chains: A, B
    EC Number: 5.3.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: IDI OR B2889
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: IPP ISOMERASE, ISOPENTENYL PYROPHOSPHATE ISOMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1DPO2Ligand/IonDIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:25 , HIS A:32 , HIS A:69 , GLU A:114 , GLU A:116BINDING SITE FOR RESIDUE MN A 201
2AC2SOFTWAREHIS B:25 , HIS B:32 , HIS B:69 , GLU B:114 , GLU B:116BINDING SITE FOR RESIDUE MN B 201
3AC3SOFTWARECYS A:67 , GLU A:87 , DPO A:301 , HOH A:501 , HOH A:502BINDING SITE FOR RESIDUE MG A 401
4AC4SOFTWARECYS B:67 , GLU B:87 , DPO B:301 , HOH B:513 , HOH B:514BINDING SITE FOR RESIDUE MG B 401
5AC5SOFTWARELYS A:21 , ARG A:51 , LYS A:55 , CYS A:67 , HIS A:69 , ARG A:83 , GLU A:87 , MG A:401 , HOH A:501 , HOH A:502 , HOH A:515 , HOH A:548 , HOH A:1503 , HOH A:1511BINDING SITE FOR RESIDUE DPO A 301
6AC6SOFTWARELYS B:21 , ARG B:51 , LYS B:55 , CYS B:67 , HIS B:69 , ARG B:83 , GLU B:87 , MG B:401 , HOH B:508 , HOH B:513 , HOH B:606 , HOH B:1505BINDING SITE FOR RESIDUE DPO B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PVF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.IDI_ECOLI30-164
 		  2A:30-164
B:30-164

(-) Exons   (0, 0)

(no "Exon" information available for 1PVF)

(-) 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:176
 aligned with IDI_ECOLI | Q46822 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:176
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      
            IDI_ECOLI     4 EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFT 179
               SCOP domains d1pvfa_ A: Isopentenyl diphosphate isomerase                                                                                                                                     SCOP domains
               CATH domains 1pvfA00 A:4-179 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeeeehhhhh......ee.eeeeee.....eeeeee..........ee..eee......hhhhhhhhhhhhhhh......eeee...eeeee.....eeeee..eeeee...........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------NUDIX  PDB: A:30-164 UniProt: 30-164                                                                                                   --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pvf A   4 EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFT 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      


Chain B from PDB  Type:PROTEIN  Length:180
 aligned with IDI_ECOLI | Q46822 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:180
                                                                                                                                                                                                            182 
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173        |-
            IDI_ECOLI     4 EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFTQLK-   -
               SCOP domains d1pvfb_ B: Isopentenyl diphosphate isomerase                                                                                                                                         SCOP domains
               CATH domains 1pvfB00 B:4-183 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                         CATH domains
           Pfam domains (1) ---------------------------NUDIX-1pvfB01 B:31-165                                                                                                                 ------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------NUDIX-1pvfB02 B:31-165                                                                                                                 ------------------ Pfam domains (2)
         Sec.struct. author .eeeee.....eeeeeehhhhh......ee.eeeeee.....eeeeee..........ee..eee......hhhhhhhhhhhhhhh......eeee...eeeee.....eeeee..eeeee...........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------NUDIX  PDB: B:30-164 UniProt: 30-164                                                                                                   ------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pvf B   4 EHVILLNAQGVPTGTLEKYAAHTADTRLHLAFSSWLFNAKGQLLVTRRALSKKAWPGVWTNSVCGHPQLGESNEDAVIRRCRYELGVEITPPESIYPDFRYRATDPSGIVENEVCPVFAARTTSALQINDDEVMDYQWCDLADVLHGIDATPWAFSPWMVMQATNREARKRLSAFTQLKL 183
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183
   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) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NUDIX (85)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (IDI_ECOLI | Q46822)
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:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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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  1pvf
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  IDI_ECOLI | Q46822
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  5.3.3.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        IDI_ECOLI | Q46822: 1hx3 1hzt 1i9a 1nfs 1nfz 1ow2 1ppv 1ppw 1q54 1r67 1x83 1x84 2b2k 2g73 2g74 2vnp 2vnq

(-) Related Entries Specified in the PDB File

1hx3 WILDTYPE PROTEIN IN THE PRESENCE OF METAL
1hzt METAL FREE WILDTYPE PROTEIN
1n2u C67A MUTANT IN COMPLEX WITH BROMOHYDRINE OF IPP
1nfs WILDTYPE PROTEIN IN COMPLEX WITH NIPP
1nfz WILDTYPE PROTEIN IN COMPLEX WITH EIPP