Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  E. COLI UNDECAPRENYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH BPH-629
 
Authors :  R. T. Guo, T. P. Ko, R. Cao, P. H. Liang, E. Oldfield, A. H. J. Wang
Date :  24 Jan 07  (Deposition) - 12 Jun 07  (Release) - 17 Jun 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Wall, Prenyltransferase, Farnesyl Pyrophosphate, Bisphosphonate, Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. T. Guo, R. Cao, P. H. Liang, T. P. Ko, T. H. Chang, M. P. Hudock, W. Y. Jeng, C. K. M. Chen, Y. Zhang, Y. Song, C. J. Kuo, F. Yin, E. Oldfield, A. H. J. Wang
Bisphosphonates Target Multiple Sites In Both Cis- And Trans-Prenyltransferases
Proc. Natl. Acad. Sci. Usa V. 104 10022 2007
PubMed-ID: 17535895  |  Reference-DOI: 10.1073/PNAS.0702254104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNDECAPRENYL PYROPHOSPHATE SYNTHETASE
    Chains: A, B
    EC Number: 2.5.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32/LIC
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: UPP SYNTHETASE, 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, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1B297Ligand/Ion[2-(3-DIBENZOFURAN-4-YL-PHENYL)-1-HYDROXY-1-PHOSPHONO-ETHYL]-PHOSPHONIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:25 , ASP A:26 , GLY A:27 , ASN A:28 , GLY A:29 , ARG A:39 , HIS A:43 , ALA A:47 , ALA A:69 , PHE A:70 , SER A:71 , SER A:72 , GLU A:73 , ARG A:77 , B29 A:502 , B29 A:504 , HOH A:542BINDING SITE FOR RESIDUE B29 A 501
2AC2SOFTWAREARG A:39 , HIS A:43 , SER A:71 , ARG A:77 , GLU A:81 , LEU A:85 , B29 A:501 , B29 A:503 , HOH A:595 , HOH A:597 , HOH A:598 , ASN B:234 , ASN B:238 , ARG B:241 , HOH B:621BINDING SITE FOR RESIDUE B29 A 502
3AC3SOFTWARETYR A:68 , ALA A:69 , ASN A:74 , VAL A:82 , LEU A:85 , MET A:86 , PHE A:89 , ALA A:143 , ASN A:144 , TYR A:145 , B29 A:502 , B29 A:504 , HOH A:534 , HOH A:536 , HOH A:537BINDING SITE FOR RESIDUE B29 A 503
4AC4SOFTWAREARG A:51 , VAL A:54 , SER A:55 , ALA A:92 , LEU A:93 , GLU A:96 , SER A:99 , LEU A:100 , HIS A:103 , ILE A:141 , B29 A:501 , B29 A:503 , HOH A:715BINDING SITE FOR RESIDUE B29 A 504
5AC5SOFTWAREMET B:25 , ASP B:26 , GLY B:27 , ASN B:28 , GLY B:29 , ARG B:39 , HIS B:43 , ALA B:69 , PHE B:70 , SER B:71 , B29 B:506 , HOH B:558BINDING SITE FOR RESIDUE B29 B 505
6AC6SOFTWAREALA B:40 , HIS B:43 , ALA B:69 , LEU B:88 , B29 B:505 , HOH B:527BINDING SITE FOR RESIDUE B29 B 506
7AC7SOFTWAREILE B:38 , ARG B:39 , ARG B:102 , HIS B:103BINDING SITE FOR RESIDUE B29 B 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E98)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2E98)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E98)

(-) 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 2E98)

(-) 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:226
 aligned with UPPS_ECOLI | P60472 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:226
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      
           UPPS_ECOLI    15 AHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE 240
               SCOP domains d2e98a_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains 2e98A00 A:15-240  [code=3.40.1180.10, no name defined]                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...........eeee...........hhhhh..eeee...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      --------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e98 A  15 AHGCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRE 240
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234      


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with UPPS_ECOLI | P60472 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:227
                                    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 GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSSENWNRPAQEVSALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRERRF 243
               SCOP domains d2e98b_ B: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains 2e98B00 B:17-243  [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...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e98 B  17 GCRHVAIIMDGNGRWAKKQGKIRAFGHKAGAKSVRRAVSFAANNGIEALTLYAFSS----------SALMELFVWALDSEVKSLHRHNVRLRIIGDTSRFNSRLQERIRKSEALTAGNTGLTLNIAANYGGRWDIVQGVRQLAEKVQQGNLQPDQIDEEMLNQHVCMHELAPVDLVIRTGGEHRISNFLLWQIAYAELYFTDVLWPDFDEQDFEGALNAFANRERRF 243
                                    26        36        46        56        66     |   -      | 86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       
                                                                                  72         83
   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  (0, 0)

(no "Pfam Domain" information available for 2E98)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    B29  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2e98)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2e98
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  UPPS_ECOLI | P60472
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.5.1.31
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  UPPS_ECOLI | P60472
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        UPPS_ECOLI | P60472: 1jp3 1ueh 1v7u 1x06 1x07 1x08 1x09 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

1x06 WILD-TYPE UPPS IN COMPLEX WITH MG, FSPP AND IPP
1x07 WILD-TYPE UPPS IN COMPLEX WITH MG AND IPP
1x08 D26A MUTANT UPPS IN COMPLEX WITH MG, FSPP AND IPP
1x09 D26A MUTANT UPPS IN COMPLEX WITH MG AND IPP
2e99 THE SAME PROTEIN COMPLEX WITH BPH-608
2e9a THE SAME PROTEIN COMPLEX WITH BPH-628
2e9c THE SAME PROTEIN COMPLEX WITH BPH-675
2e9d THE SAME PROTEIN COMPLEX WITH BPH-676