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(-) Description

Title :  E. COLI UNDECAPRENYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH TRITON X-100, MAGNESIUM AND SULFATE
 
Authors :  S. -Y. Chang, T. -P. Ko, P. -H. Liang, A. H. -J. Wang
Date :  15 May 03  (Deposition) - 12 Aug 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Parallel Alpha-Beta, Rossmann-Like Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. -Y. Chang, T. -P. Ko, P. -H. Liang, A. H. -J. Wang
Catalytic Mechanism Revealed By The Crystal Structure Of Undecaprenyl Pyrophosphate Synthase In Complex With Sulfate Magnesium, And Triton
J. Biol. Chem. V. 278 29298 2003
PubMed-ID: 12756244  |  Reference-DOI: 10.1074/JBC.M302687200

(-) Compounds

Molecule 1 - UNDECAPRENYL PYROPHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32XA-LIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2OXN2Ligand/IonOXTOXYNOL-10
3SO45Ligand/IonSULFATE ION
4UNL1Ligand/IonUNKNOWN LIGAND

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:27 , ASN A:28 , GLY A:29 , ARG A:30 , ARG A:39 , HOH A:1170BINDING SITE FOR RESIDUE SO4 A 901
02AC2SOFTWAREARG A:194 , ARG A:200 , SER A:202 , ARG B:241BINDING SITE FOR RESIDUE SO4 A 902
03AC3SOFTWAREGLY B:27 , ASN B:28 , GLY B:29 , ARG B:30 , HOH B:1037BINDING SITE FOR RESIDUE SO4 B 903
04AC4SOFTWAREARG B:194 , ARG B:200 , SER B:202 , HOH B:1038BINDING SITE FOR RESIDUE SO4 B 904
05AC5SOFTWARELYS B:33 , ARG B:102 , HOH B:973 , HOH B:1163 , HOH B:1261BINDING SITE FOR RESIDUE SO4 B 905
06AC6SOFTWAREHIS A:199 , HOH A:1205 , HOH A:1206 , GLU B:213 , HOH B:1292 , HOH B:1293BINDING SITE FOR RESIDUE MG A 701
07AC7SOFTWAREGLU A:213 , HOH A:1207 , HOH A:1208 , HIS B:199 , HOH B:1294 , HOH B:1295BINDING SITE FOR RESIDUE MG A 702
08AC8SOFTWAREVAL B:54 , SER B:55 , ASN B:59 , GLU B:96 , HIS B:103 , OXN B:802BINDING SITE FOR RESIDUE OXN B 801
09AC9SOFTWAREMET B:25 , ASN B:28 , HIS B:43 , GLY B:46 , ALA B:47 , ALA B:69 , ILE B:109 , ALA B:143 , TRP B:221 , OXN B:801BINDING SITE FOR RESIDUE OXN B 802
10BC1SOFTWAREILE B:38 , ARG B:39 , SER B:99 , ARG B:102 , HIS B:103 , HOH B:948BINDING SITE FOR RESIDUE UNL B 803

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1UEH)

(-) 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 d1ueha_ A: Undecaprenyl diphosphate synthase                                                                                                                                                                                         SCOP domains
               CATH domains 1uehA00 A:13-240  [code=3.40.1180.10, no name defined]                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.--------------hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...........eeee...........hhhhh..eeee...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ueh 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        
                                                                                     71             86                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with UPPS_ECOLI | P60472 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:225
                                    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 GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRER 241
               SCOP domains d1uehb_ B: Undecaprenyl diphosphate synthase                                                                                                                                                                                      SCOP domains
               CATH domains 1uehB00 B:17-241  [code=3.40.1180.10, no name defined]                                                                                                                                                                            CATH domains
           Pfam domains (1) -------Prenyltransf-1uehB01 B:24-241                                                                                                                                                                                              Pfam domains (1)
           Pfam domains (2) -------Prenyltransf-1uehB02 B:24-241                                                                                                                                                                                              Pfam domains (2)
         Sec.struct. author ...eeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...........eeeee..........hhhhh..eeee...hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      ---------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ueh B  17 GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRER 241
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236
   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) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Prenyltransf] (8)

(-) 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 | P60472: 1jp3 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

1jp3 APO-ENZYME STRUCTURE DETERMINED BY SAD METHOD USING SE-MET