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(-) Description

Title :  CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM HYPERTHERMOPHILIC THERMOTOGA MARITIMA A76Y/S77F MUTANT
 
Authors :  R. T. Guo, C. J. Kuo, T. P. Ko, C. C. Chou, P. H. Liang, A. H. -J. Wang
Date :  23 Apr 04  (Deposition) - 18 May 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (8x)
Keywords :  Trans-Type Prenyltransferase, Thermophilic, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. T. Guo, C. J. Kuo, T. P. Ko, C. C. Chou, P. H. Liang, A. H. -J. Wang
A Molecular Ruler For Chain Elongation Catalyzed By Octaprenyl Pyrophosphate Synthase And Its Structure-Based Engineering To Produce Unprecedented Long Chain Trans-Preny Products
Biochemistry V. 43 7678 2004
PubMed-ID: 15196010  |  Reference-DOI: 10.1021/BI036336D

(-) Compounds

Molecule 1 - OCTOPRENYL-DIPHOSPHATE SYNTHASE
    Chains: A
    EC Number: 2.5.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET32XA-LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: TRANS-OCTAPRENYLTRANSTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (2x): A
Biological Unit 3 (8x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:40 , LYS A:41 , HIS A:74 , ARG A:91 , HOH A:556 , HOH A:557 , HOH A:558BINDING SITE FOR RESIDUE SO4 A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VG3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VG3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VG3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VG3)

(-) Exons   (0, 0)

(no "Exon" information available for 1VG3)

(-) Sequences/Alignments

Asymmetric 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:279
 aligned with Q9X1M1_THEMA | Q9X1M1 from UniProtKB/TrEMBL  Length:299

    Alignment length:279
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278         
         Q9X1M1_THEMA     9 NSYELEKVKERIEQILSQFFPEQIMKDLPLYGKMLRVRLSILSFKNRGVEIGEDAISSLAALELVHLASLLHDDVIDGARFRRGKETINFMYGDKAAVAAGDLVLVSAFHTVEEIGNNKLRRAFLNVIGKMSEAELIEQLSRYKPITKEEYLRIVEGKSGALFGLALQLPALLEGELGEDLYNLGVTIGTIYQMFDDIMDFAGMEKIGKDGFLDLKNGVASFPLVTAMEKFPEARQMFENRDWSGLMSFMREKGILKECEETLKVLVKNVIIENSWLRD 287
               SCOP domains d1vg3a_ A: Octoprenyl-diphosphate synthase                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1vg3A00 A:9-287 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------polyprenyl_synt-1vg3A01 A:31-270                                                                                                                                                                                                                ----------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vg3 A   9 NSYELEKVKERIEQILSQFFPEQIMKDLPLYGKMLRVRLSILSFKNRGVEIGEDAISSLAALELVHLYFLLHDDVIDGARFRRGKETINFMYGDKAAVAAGDLVLVSAFHTVEEIGNNKLRRAFLNVIGKMSEAELIEQLSRYKPITKEEYLRIVEGKSGALFGLALQLPALLEGELGEDLYNLGVTIGTIYQMFDDIMDFAGMEKIGKDGFLDLKNGVASFPLVTAMEKFPEARQMFENRDWSGLMSFMREKGILKECEETLKVLVKNVIIENSWLRD 287
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278
   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, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: polyprenyl_synt] (86)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9X1M1_THEMA | Q9X1M1)
molecular function
    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.
biological process
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.

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  1vg3
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  2.5.1.11
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 Related Entries

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

UniProtKB/TrEMBL
        Q9X1M1_THEMA | Q9X1M1: 1v4e 1v4h 1v4i 1v4j 1v4k 1vg2 1vg4 1vg6 1vg7 1wkz 1wl0 1wl1 1wl2 1wl3 2azl

(-) Related Entries Specified in the PDB File

1v4e THE SAME PROTEIN (WILD-TYPE)
1v4h THE SAME PROTEIN (F52A MUTANT)
1v4i THE SAME PROTEIN (F132A MUTANT)
1v4j THE SAME PROTEIN (V73Y MUTANT)
1v4k THE SAME PROTEIN (S77F MUTANT)
1vg2 THE SAME PROTEIN (A76Y MUTANT)
1vg4 THE SAME PROTEIN (F132A/L128A MUTANT)
1vg6 THE SAME PROTEIN (F132A/L128A/I123A MUTANT)
1vg7 THE SAME PROTEIN (F132A/L128A/I123A/D62A MUTANT)