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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI UNDECAPRENYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH BPH-1299
 
Authors :  R. Cao, Y. -L. Liu, E. Oldfield
Date :  15 Jun 11  (Deposition) - 19 Dec 12  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Zhu, Y. Zhang, W. Sinko, M. E. Hensler, J. Olson, K. J. Molohon, S. Lindert, R. Cao, K. Li, K. Wang, Y. Wang, Y. L. Liu, A. Sankovsky, C. A. De Oliveira, D. A. Mitchell, V. Nizet, J. A. Mccammon, E. Oldfiel
Antibacterial Drug Leads Targeting Isoprenoid Biosynthesis.
Proc. Natl. Acad. Sci. Usa V. 110 123 2013
PubMed-ID: 23248302  |  Reference-DOI: 10.1073/PNAS.1219899110

(-) Compounds

Molecule 1 - UNDECAPRENYL PYROPHOSPHATE SYNTHASE
    Chains: B, A
    EC Number: 2.5.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UPPS, C0211
    Organism Scientific: ESCHERICHIA COLI O6
    Organism Taxid: 217992
    Synonym: UPP SYNTHASE, DI-TRANS,POLY-CIS-DECAPRENYLCISTRANSFERASE, UNDECAPRENYL DIPHOSPHATE SYNTHASE, UDS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1P091Ligand/Ion2-{[4-(3,4-DIMETHYLPHENOXY)PHENYL]CARBAMOYL}BENZOICACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU B:85 , PHE B:89 , ALA B:92 , LEU B:93 , PHE B:116 , ALA B:142 , ALA B:143 , ASN B:144 , HOH B:313 , HOH B:353BINDING SITE FOR RESIDUE P09 B 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SGT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SGT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SGT)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPP_SYNTHASEPS01066 Undecaprenyl pyrophosphate synthase family signature.UPPS_ECOL6190-207
 		  2A:190-207
B:190-207

(-) Exons   (0, 0)

(no "Exon" information available for 3SGT)

(-) 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:206
 aligned with UPPS_ECOL6 | P60473 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:223
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236   
           UPPS_ECOL6    17 GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANR 239
               SCOP domains d3sgta_ A: Undecaprenyl diphosphate synthase                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeee...-----------------hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...........eeee...........hhhhh..eeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      -------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sgt A  17 GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFS-----------------FVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANR 239
                                    26        36        46        56        66    |    -         -  |     96       106       116       126       136       146       156       166       176       186       196       206       216       226       236   
                                                                                 71                89                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with UPPS_ECOL6 | P60473 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_ECOL6    13 LPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE 240
               SCOP domains d3sgtb_ B: Undecaprenyl diphosphate synthase                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....---hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...........eeee...........hhhhh..eeee...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      --------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3sgt B  13 LPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSEN---PAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE 240
                                    22        32        42        52        62        72 |   |  82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232        
                                                                                        74  78
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "CATH Domain" information available for 3SGT)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (UPPS_ECOL6 | P60473)
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: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:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.

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