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(-) Description

Title :  CRYSTAL STRUCTURE OF UNDECAPRENYL DIPHOSPHATE SYNTHASE FROM MICROCOCCUS LUTEUS B-P 26
 
Authors :  M. Fujihashi, Y. -W. Zhang, Y. Higuchi, X. -Y. Li, T. Koyama, K. Miki
Date :  26 Jun 00  (Deposition) - 28 Mar 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Parallel Beta Sheet, New Fold For Isoprenoid Synthase, Peptidoglycan Synthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Fujihashi, Y. W. Zhang, Y. Higuchi, X. Y. Li, T. Koyama, K. Miki
Crystal Structure Of Cis-Prenyl Chain Elongating Enzyme, Undecaprenyl Diphosphate Synthase.
Proc. Natl. Acad. Sci. Usa V. 98 4337 2001
PubMed-ID: 11287651  |  Reference-DOI: 10.1073/PNAS.071514398
(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: PMLUEX3
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: MICROCOCCUS LUTEUS
    Organism Taxid: 1270

 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
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:29 , GLY A:30 , ASN A:31 , GLY A:32 , ARG A:33 , ARG A:42BINDING SITE FOR RESIDUE SO4 A 901
2AC2SOFTWAREASP B:29 , GLY B:30 , ASN B:31 , GLY B:32 , ARG B:33BINDING SITE FOR RESIDUE SO4 B 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F75)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F75)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F75)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UPP_SYNTHASEPS01066 Undecaprenyl pyrophosphate synthase family signature.UPPS_MICLU193-210
 		  2A:193-210
B:193-210

(-) Exons   (0, 0)

(no "Exon" information available for 1F75)

(-) 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
 aligned with UPPS_MICLU | O82827 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:229
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233         
           UPPS_MICLU    14 NINAAQIPKHIAIIMDGNGRWAKQKKMPRIKGHYEGMQTVKKITRYASDLGVKYLTLYAFSTENWSRPKDEVNYLMKLPGDFLNTFLPELIEKNVKVETIGFIDDLPDHTKKAVLEAKEKTKHNTGLTLVFALNYGGRKEIISAVQLIAERYKSGEISLDEISETHFNEYLFTANMPDPELLIRTSGEERLSNFLIWQCSYSEFVFIDEFWPDFNEESLAQCISIYQNR 242
               SCOP domains d1f75a_ A: Undecaprenyl diphosphate synthase                                                                                                                                                                                          SCOP domains
               CATH domains 1f75A00 A:14-242  [code=3.40.1180.10, no name defined]                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.------------hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........eeee..................eeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      -------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f75 A  14 NINAAQIPKHIAIIMDGNGRWAKQKKMPRIKGHYEGMQTVRKITRYASDLGVKYLTLYAF------------NYLMKLPGDFLNTFLPELIEKNVKVETIGFIDDLPDHTKKAVLEAKEKTKHNTGLTLVFALNYGGRKEIISAVQLIAERYKSGEISLDEISETHFNEYLFTANMPDPELLIRTSGEERLSNFLIWQCSYSEFVFIDEFWPDFNEESLAQCISIYQNR 242
                                    23        33        43        53        63        73         -  |     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233         
                                                                                      73           86                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:212
 aligned with UPPS_MICLU | O82827 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:224
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238    
           UPPS_MICLU    19 QIPKHIAIIMDGNGRWAKQKKMPRIKGHYEGMQTVKKITRYASDLGVKYLTLYAFSTENWSRPKDEVNYLMKLPGDFLNTFLPELIEKNVKVETIGFIDDLPDHTKKAVLEAKEKTKHNTGLTLVFALNYGGRKEIISAVQLIAERYKSGEISLDEISETHFNEYLFTANMPDPELLIRTSGEERLSNFLIWQCSYSEFVFIDEFWPDFNEESLAQCISIYQNR 242
               SCOP domains d1f75b_ B: Undecaprenyl diphosphate synthase                                                                                                                                                                                     SCOP domains
               CATH domains 1f75B00 B:19-242  [code=3.40.1180.10, no name defined]                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.------------....hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhh.........eeee..................eeee...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UPP_SYNTHASE      -------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f75 B  19 QIPKHIAIIMDGNGRWAKQKKMPRIKGHYEGMQTVRKITRYASDLGVKYLTLYAF------------NYLMKLPGDFLNTFLPELIEKNVKVETIGFIDDLPDHTKKAVLEAKEKTKHNTGLTLVFALNYGGRKEIISAVQLIAERYKSGEISLDEISETHFNEYLFTANMPDPELLIRTSGEERLSNFLIWQCSYSEFVFIDEFWPDFNEESLAQCISIYQNR 242
                                    28        38        48        58        68    |    -       |88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238    
                                                                                 73           86
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 1F75)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (UPPS_MICLU | O82827)
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).

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  1f75
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