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(-) Description

Title :  STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH EIPP
 
Authors :  J. Wouters
Date :  16 Dec 02  (Deposition) - 24 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Complex, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Wouters, Y. Oudjama, S. J. Barkley, C. Tricot, V. Stalon, L. Droogmans, C. D. Poulter
Catalytic Mechanism Of Escherichia Coli Isopentenyl Diphosphate Isomerase Involves Cys-67, Glu-116, And Tyr-104 As Suggested By Crystal Structures Of Complexes With Transition State Analogues And Irreversible Inhibitors
J. Biol. Chem. V. 278 11903 2003
PubMed-ID: 12540835  |  Reference-DOI: 10.1074/JBC.M212823200
(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
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: DIMETHYLALLYL DIPHOSPHATE ISOMERASE, 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
1EIP2Ligand/Ion4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE
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 , EIP A:301 , HOH A:508 , HOH A:509BINDING SITE FOR RESIDUE MG A 401
4AC4SOFTWARECYS B:67 , GLU B:87 , EIP B:302 , HOH B:519 , HOH B:520BINDING SITE FOR RESIDUE MG B 401
5AC5SOFTWARELYS A:21 , ARG A:51 , LYS A:55 , CYS A:67 , GLY A:68 , HIS A:69 , ARG A:83 , GLU A:87 , TYR A:104 , GLU A:114 , GLU A:116 , MG A:401 , HOH A:506 , HOH A:508 , HOH A:509 , HOH A:641BINDING SITE FOR RESIDUE EIP A 301
6AC6SOFTWARELYS B:21 , ARG B:51 , LYS B:55 , CYS B:67 , GLY B:68 , HIS B:69 , ARG B:83 , GLU B:87 , TYR B:104 , GLU B:114 , GLU B:116 , TRP B:161 , MG B:401 , HOH B:513 , HOH B:520 , HOH B:774BINDING SITE FOR RESIDUE EIP B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1NFZ)

(-) 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 d1nfza_ A: Isopentenyl diphosphate isomerase                                                                                                                                     SCOP domains
               CATH domains 1nfzA00 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...........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------NUDIX  PDB: A:30-164 UniProt: 30-164                                                                                                   --------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nfz 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 d1nfzb_ B: Isopentenyl diphosphate isomerase                                                                                                                                         SCOP domains
               CATH domains 1nfzB00 B:4-183 Nucleoside Triphosphate Pyrophosphohydrolase                                                                                                                         CATH domains
           Pfam domains (1) ---------------------------NUDIX-1nfzB01 B:31-165                                                                                                                 ------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------NUDIX-1nfzB02 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
                 1nfz 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)
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  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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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1hx3 METAL BOUND PROTEIN
1hzt UNCOMPLEXED PROTEIN
1n2u C67A MUTANT COMPLEXED WITH THE BROMOHYDRINE OF IPP