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(-) Description

Title :  STRUCTURE OF E.COLI UNDECAPRENYL PYROPHOSPHATE SYNTHASE
 
Authors :  T. P. Ko, Y. K. Chen, H. Robinson, P. C. Tsai, Y. G. Gao, A. P. C. Chen, A. H. J. Wang, P. H. Liang
Date :  31 Jul 01  (Deposition) - 15 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Hydrophobic Tunnel, Product Chain Length, Flexible Loop, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. P. Ko, Y. K. Chen, H. Robinson, P. C. Tsai, Y. G. Gao, A. P. Chen, A. H. Wang, P. H. Liang
Mechanism Of Product Chain Length Determination And The Role Of A Flexible Loop In Escherichia Coli Undecaprenyl-Pyrophosphate Synthase Catalysis.
J. Biol. Chem. V. 276 47474 2001
PubMed-ID: 11581264  |  Reference-DOI: 10.1074/JBC.M106747200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNDECAPRENYL PYROPHOSPHATE SYNTHASE
    ChainsA, B
    EC Number2.5.1.31
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET32XA-LIC
    Expression System StrainB834
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1EGC1Ligand/Ion2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-TETRAMETHYL-BUTYL)-PHENOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMSE A:86 , PHE A:89 , GLU A:96 , HOH A:807BINDING SITE FOR RESIDUE EGC A 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JP3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JP3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JP3)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPP_SYNTHASEPS01066 Undecaprenyl pyrophosphate synthase family signature.UPPS_ECOLI190-207
 
  2A:190-207
B:190-207

(-) Exons   (0, 0)

(no "Exon" information available for 1JP3)

(-) 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:214
 aligned with UPPS_ECOLI | P60472 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:228
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232        
           UPPS_ECOLI    13 LPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE 240
               SCOP domains d1jp3a_ A: Undecaprenyl diphosphate synthase                                                                                                                                                                                         SCOP domains
               CATH domains 1jp3A00 A:13-240  [code=3.40.1180.10, no name defined]                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..--------------hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...........eeee...........hhhhh..eeee...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jp3 A  13 LPAHGCRHVAIImDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFS--------------mELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEmLNQHVCmHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE 240
                                    22  |     32        42        52        62        |-         -   |    92       102       112       122       132       142       152       162       172   |   182|      192       202       212       222       232        
                                       25-MSE                                        71             86-MSE                                                                                   176-MSE  |                                                         
                                                                                                                                                                                                    183-MSE                                                     

Chain B from PDB  Type:PROTEIN  Length:211
 aligned with UPPS_ECOLI | P60472 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:222
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236  
           UPPS_ECOLI    17 GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFAN 238
               SCOP domains d1jp3b_ B: Undecaprenyl diphosphate synthase                                                                                                                                                                                   SCOP domains
               CATH domains 1jp3B00 B:17-238  [code=3.40.1180.10, no name defined]                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..-----------hhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...........eeee...........hhhhh..eeee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      ------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jp3 B  17 GCRHVAIImDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFS-----------SALmELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEmLNQHVCmHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFAN 238
                                    26        36        46        56        66    |    -      | 86        96       106       116       126       136       146       156       166       176      |186       196       206       216       226       236  
                                   25-MSE                                        71          83  |                                                                                       176-MSE  |                                                       
                                                                                                86-MSE                                                                                          183-MSE                                                   

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1JP3)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (UPPS_ECOLI | P60472)
molecular function
    GO:0008834    di-trans,poly-cis-decaprenylcistransferase activity    Catalysis of the reaction: di-trans-poly-cis-decaprenyl diphosphate + isopentenyl diphosphate = diphosphate + di-trans-poly-cis-undecaprenyl diphosphate.
    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:0004659    prenyltransferase activity    Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
    GO:0043164    Gram-negative-bacterium-type cell wall biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall of the type found in Gram-negative bacteria. The cell wall is the rigid or semi-rigid envelope lying outside the cell membrane.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0016094    polyprenol biosynthetic process    The chemical reactions and pathways resulting in the formation of polyprenols, prenols with more than 4 isoprenoid residues, which may be all-trans, or a mixture of cis and trans.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UPPS_ECOLI | P604721ueh 1v7u 1x06 1x07 1x08 1x09 2e98 2e99 2e9a 2e9c 2e9d 3qas 3sgv 3sgx 3sh0 3th8 3wyj 4h2j 4h2m 4h2o 4h38 4h3a 4h3c 5cqb 5cqj

(-) Related Entries Specified in the PDB File

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