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(-) Description

Title :  CRYSTAL STRUCTURE OF (S)-3-O-GERANYLGERANYLGLYCERYL PHOSPHATE SYNTHASE COMPLEXED WITH CITRATE
 
Authors :  J. Payandeh
Date :  29 Nov 05  (Deposition) - 24 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Non-Canonical Tim-Barrel; Prenyltransferase; Archaeal Lipid Synthesis; Dimer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Payandeh, M. Fujihashi, W. Gillon, E. F. Pai
The Crystal Structure Of (S)-3-O-Geranylgeranylglyceryl Phosphate Synthase Reveals An Ancient Fold For An Ancient Enzyme
J. Biol. Chem. V. 281 6070 2006
PubMed-ID: 16377641  |  Reference-DOI: 10.1074/JBC.M509377200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - (S)-3-O-GERANYLGERANYLGLYCERYL PHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: GGGPS
    Gene: PCRB
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Other Details: THREE AMINO ACIDS REMAIN AFTER REMOVAL OF THE HIS-TAG, GSH
    Synonym: GGGPS;
PROTEIN PCRB HOMOLOG

 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
1CIT2Ligand/IonCITRIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:5 , HOH A:10 , HOH A:258 , LYS A:1011 , TYR A:1165 , GLU A:1167 , SER A:1169 , GLY A:1170 , GLY A:1193 , GLY A:1195 , ILE A:1213 , GLY A:1215 , ASN A:1216BINDING SITE FOR RESIDUE CIT A 3001
2AC2SOFTWAREHOH B:9 , HOH B:32 , HOH B:280 , LYS B:2011 , TYR B:2165 , GLU B:2167 , SER B:2169 , GLY B:2170 , GLY B:2193 , GLY B:2194 , GLY B:2195 , ILE B:2213 , GLY B:2215 , ASN B:2216BINDING SITE FOR RESIDUE CIT B 3002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F6U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F6U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F6U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2F6U)

(-) Exons   (0, 0)

(no "Exon" information available for 2F6U)

(-) 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:231
 aligned with GGGPS_ARCFU | O29844 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
         GGGPS_ARCFU      1 MRWRKWRHITKLDPDRTNTDEIIKAVADSGTDAVMISGTQNVTYEKARTLIEKVSQYGLPIVVEPSDPSNVVYDVDYLFVPTVLNSADGDWITGKHAQWVRMHYENLQKFTEIIESEFIQIEGYIVLNPDSAVARVTKALCNIDKELAASYALVGEKLFNLPIIYIEYSGTYGNPELVAEVKKVLDKARLFYGGGIDSREKAREMLRYADTIIVGNVIYEKGIDAFLETLP  231
               SCOP domains d2f6ua1 A:1001-1231 (S)-3-O-geranylgeranylglyceryl phosphate synthase                                                                                                                                                                   SCOP domains
               CATH domains 2f6uA00 A:1001-1231 FMN-linked oxidoreductases                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eeeee......hhhhhhhhhh....eeee......hhhhhhhhhhhhh.....eee.............eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....hhhhhhh......hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhh...eeeee....hhhhhhhhhhhh.eeeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2f6u A 1001 MRWRKWRHITKLDPDRTNTDEIIKAVADSGTDAVMISGTQNVTYEKARTLIEKVSQYGLPIVVEPSDPSNVVYDVDYLFVPTVLNSADGDWITGKHAQWVRMHYENLQKFTEIIESEFIQIEGYIVLNPDSAVARVTKALCNIDKELAASYALVGEKLFNLPIIYIEYSGTYGNPELVAEVKKVLDKARLFYGGGIDSREKAREMLRYADTIIVGNVIYEKGIDAFLETLP 1231
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230 


Chain B from PDB  Type:PROTEIN  Length:231
 aligned with GGGPS_ARCFU | O29844 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 
         GGGPS_ARCFU      1 MRWRKWRHITKLDPDRTNTDEIIKAVADSGTDAVMISGTQNVTYEKARTLIEKVSQYGLPIVVEPSDPSNVVYDVDYLFVPTVLNSADGDWITGKHAQWVRMHYENLQKFTEIIESEFIQIEGYIVLNPDSAVARVTKALCNIDKELAASYALVGEKLFNLPIIYIEYSGTYGNPELVAEVKKVLDKARLFYGGGIDSREKAREMLRYADTIIVGNVIYEKGIDAFLETLP  231
               SCOP domains d2f6ub_ B: (S)-3-O-geranylgeranylglyceryl phosphate synthase                                                                                                                                                                            SCOP domains
               CATH domains 2f6uB00 B:2001-2231 FMN-linked oxidoreductases                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.eeeee......hhhhhhhhhhh...eeee......hhhhhhhhhhhhhh....eee.............eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....hhhhhhhh.....hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhh...eeeee....hhhhhhhhh....eeeehhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2f6u B 2001 MRWRKWRHITKLDPDRTNTDEIIKAVADSGTDAVMISGTQNVTYEKARTLIEKVSQYGLPIVVEPSDPSNVVYDVDYLFVPTVLNSADGDWITGKHAQWVRMHYENLQKFTEIIESEFIQIEGYIVLNPDSAVARVTKALCNIDKELAASYALVGEKLFNLPIIYIEYSGTYGNPELVAEVKKVLDKARLFYGGGIDSREKAREMLRYADTIIVGNVIYEKGIDAFLETLP 2231
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100      2110      2120      2130      2140      2150      2160      2170      2180      2190      2200      2210      2220      2230
   Legend:   → Mismatch (orange background)
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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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F6U)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GGGPS_ARCFU | O29844)
molecular function
    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:0047294    phosphoglycerol geranylgeranyltransferase activity    Catalysis of the reaction: sn-glycerol 1-phosphate + all-trans-geranylgeranyl diphosphate = sn-3-O-(geranylgeranyl)glycerol 1-phosphate + diphosphate.
    GO:0002094    polyprenyltransferase activity    Catalysis of the transfer of multiple prenyl groups 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:0046474    glycerophospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.
    GO:0006650    glycerophospholipid metabolic process    The chemical reactions and pathways involving glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0008654    phospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  2.5.1.42
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 Related Entries

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        GGGPS_ARCFU | O29844: 2f6x

(-) Related Entries Specified in the PDB File

1viz CRYSTAL STRUCTURE OF PCRB, A BACTERIAL PROTEIN OF UNKNOWN FUNCTION
2f6x