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(-) Description

Title :  STRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHATE SYNTHASE IN COMPLEX WITH BPH-1354
 
Authors :  W. Zhu, E. Oldfield
Date :  12 Sep 12  (Deposition) - 19 Dec 12  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Prenyl Transferase Inhibitor Complex, Alpha-Helix, Prenyl Transferase, Cell Wall Biosynthesis, Farnesyl Diphosphate Binding, Isopentenyl Diphosphate Binding, 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: A, B
    EC Number: 2.5.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UPPS, ISPU, RTH, YAES, B0174, JW0169
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: UPP SYNTHASE, DI-TRANS,POLY-CIS-DECAPRENYLCISTRANSFERASE, DITRANS,POLYCIS-UNDECAPRENYL-DIPHOSPHATE SYNTHASE, 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, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
10YU2Ligand/IonN~4~-[4-(4,5-DIHYDRO-1H-IMIDAZOL-2-YL)PHENYL]-N~1~-[4-(1H-IMIDAZOL-2-YL)PHENYL]-2-NITROBENZENE-1,4-DICARBOXAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:44 , ALA A:47 , VAL A:50 , ARG A:51 , VAL A:54 , SER A:55 , PHE A:89 , ALA A:92 , LEU A:93 , GLU A:96 , SER A:99 , LEU A:100 , HIS A:103 , LEU A:139 , ILE A:141BINDING SITE FOR RESIDUE 0YU A 301
2AC2SOFTWAREHIS B:43 , ALA B:47 , VAL B:50 , ARG B:51 , VAL B:54 , SER B:55 , PHE B:89 , ALA B:92 , LEU B:93 , GLU B:96 , HIS B:103 , LEU B:139BINDING SITE FOR RESIDUE 0YU B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H2J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H2J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H2J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H2J)

(-) Exons   (0, 0)

(no "Exon" information available for 4H2J)

(-) 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:217
                                                                                                                                                                                                                                                         
               SCOP domains d4h2ja_ A: Undecaprenyl diphosphate synthase                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...........eeee..................eeee...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h2j A  13 LPAHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSELMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE 240
                                    22        32        42        52        62        72||      93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       
                                                                                       73|                                                                                                                                                           
                                                                                        85                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains d4h2jb_ B: Undecaprenyl diphosphate synthase                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...........eeee...........hhhhh..eeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h2j B  17 GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSLMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANR 239
                                    26        36        46        56        66     || 88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238 
                                                                                  72|                                                                                                                                                          
                                                                                   85
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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 4H2J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H2J)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        UPPS_ECOLI | P60472: 1jp3 1ueh 1v7u 1x06 1x07 1x08 1x09 2e98 2e99 2e9a 2e9c 2e9d 3qas 3sgv 3sgx 3sh0 3th8 3wyj 4h2m 4h2o 4h38 4h3a 4h3c 5cqb 5cqj

(-) Related Entries Specified in the PDB File

4h2m 4h2o 4h38 4h3a 4h3c