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(-) Description

Title :  CRYSTAL STRUCTURE OF PCRB COMPLEXED WITH G1P FROM BACILLUS SUBTILIS SUBAP. SUBTILIS STR. 168
 
Authors :  F. Ren, X. Feng, T. P. Ko, C. H. Huang, Y. Hu, H. C. Chan, Y. L. Liu, K. Wang, C X. Pang, M. He, Y. Li, E. Oldfield, R. T. Guo
Date :  17 Oct 12  (Deposition) - 26 Dec 12  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Biosynthesis, Prenyltransferases, Enzyme Catalysis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Ren, X. Feng, T. P. Ko, C. H. Huang, Y. Hu, H. C. Chan, Y. L. Liu, K. Wang, C. C. Chen, X. Pang, M. He, Y. Li, E. Oldfield, R. T. Guo
Insights Into Tim-Barrel Prenyl Transferase Mechanisms: Crystal Structures Of Pcrb From Bacillus Subtilis And Staphylococcus Aureus
Chembiochem V. 14 195 2013
PubMed-ID: 23322418  |  Reference-DOI: 10.1002/CBIC.201200748

(-) Compounds

Molecule 1 - HEPTAPRENYLGLYCERYL PHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PCRB
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 224308
    Strain: 168
    Synonym: PCRB, HEPGP SYNTHASE, GLYCEROL-1-PHOSPHATE HEPTAPRENYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
11GP1Ligand/IonSN-GLYCEROL-1-PHOSPHATE
2CL5Ligand/IonCHLORIDE ION
3MG10Ligand/IonMAGNESIUM ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:56 , PHE A:58 , MG A:706 , HOH A:830 , HOH A:831 , HOH A:832 , HOH A:973BINDING SITE FOR RESIDUE MG A 701
02AC2SOFTWAREASP A:203 , MG A:705 , HOH A:816 , HOH A:817 , HOH A:966 , HOH A:1012 , HOH A:1089BINDING SITE FOR RESIDUE MG A 702
03AC3SOFTWAREGLY A:39 , HOH A:870 , HOH A:972 , HOH A:978 , HOH A:1043 , HOH A:1078BINDING SITE FOR RESIDUE MG A 703
04AC4SOFTWAREHOH A:941 , HOH A:974 , HOH A:975 , HOH A:1018 , HOH A:1042BINDING SITE FOR RESIDUE MG A 704
05AC5SOFTWARETHR A:5 , MG A:702 , HOH A:816 , HOH A:818 , HOH A:819 , HOH A:966 , HOH A:1030BINDING SITE FOR RESIDUE MG A 705
06AC6SOFTWAREMG A:701 , HOH A:829 , HOH A:830 , HOH A:832 , HOH A:833 , HOH A:973BINDING SITE FOR RESIDUE MG A 706
07AC7SOFTWARELEU A:59BINDING SITE FOR RESIDUE CL A 707
08AC8SOFTWARETYR A:2 , TRP A:7 , HOH A:823 , HOH A:1076BINDING SITE FOR RESIDUE CL A 708
09AC9SOFTWAREGLY A:188 , HOH A:855BINDING SITE FOR RESIDUE CL A 709
10BC1SOFTWARELEU A:19 , LYS A:54 , HOH A:882BINDING SITE FOR RESIDUE CL A 710
11BC2SOFTWARELYS B:12 , TYR B:158 , GLU B:160 , SER B:162 , GLY B:163 , GLY B:186 , GLY B:188 , GLY B:208 , ASN B:209 , HOH B:422 , HOH B:423 , HOH B:589BINDING SITE FOR RESIDUE 1GP B 301
12BC3SOFTWAREARG B:56 , PHE B:58 , HOH B:466 , HOH B:467 , HOH B:501 , HOH B:502BINDING SITE FOR RESIDUE MG B 302
13BC4SOFTWARETHR B:5 , MG B:304 , HOH B:434 , HOH B:436 , HOH B:438 , HOH B:505BINDING SITE FOR RESIDUE MG B 303
14BC5SOFTWAREASP B:203 , MG B:303 , HOH B:434 , HOH B:504 , HOH B:505 , HOH B:506 , HOH B:565BINDING SITE FOR RESIDUE MG B 304
15BC6SOFTWAREGLU A:70 , HOH A:951 , HOH A:952 , GLU B:45 , ASP B:46 , HOH B:486BINDING SITE FOR RESIDUE MG B 305
16BC7SOFTWAREGLU B:45BINDING SITE FOR RESIDUE CL B 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VZY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VZY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VZY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VZY)

(-) Exons   (0, 0)

(no "Exon" information available for 3VZY)

(-) 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 PCRB_BACSU | O34790 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
           PCRB_BACSU     1 MYDVTEWKHVFKLDPNKDLPDEQLEILCESGTDAVIIGGSDGVTEDNVLRMMSKVRRFLVPCVLEVSAIEAIVPGFDLYFIPSVLNSKNADWIVGMHQKAMKEYGELMSMEEIVAEGYCIANPDCKAAALTEADADLNMDDIVAYARVSELLQLPIFYLEYSGVLGDIEAVKKTKAVLETSTLFYGGGIKDAETAKQYAEHADVIVVGNAVYEDFDRALKTVAAVK 226
               SCOP domains d3vzya_ A: PcrB protein homolog YerE                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.eeeee........hhhhhhhh.....eee......hhhhhhhhhhhhh.....eeee..hhhhh.....eeeeeee.........hhhhhhhhhhhhhhhhhh.eeeeeeee....hhhhhhh......hhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vzy A   1 MYDVTEWKHVFKLDPNKDLPDEQLEILCESGTDAVIIGGSDGVTEDNVLRMMSKVRRFLVPCVLEVSAIEAIVPGFDLYFIPSVLNSKNADWIVGMHQKAMKEYGELMSMEEIVAEGYCIANPDCKAAALTEADADLNMDDIVAYARVSELLQLPIFYLEYSGVLGDIEAVKKTKAVLETSTLFYGGGIKDAETAKQYAEHADVIVVGNAVYEDFDRALKTVAAVK 226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      


Chain B from PDB  Type:PROTEIN  Length:228
 aligned with PCRB_BACSU | O34790 from UniProtKB/Swiss-Prot  Length:228

    Alignment length:228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        
           PCRB_BACSU     1 MYDVTEWKHVFKLDPNKDLPDEQLEILCESGTDAVIIGGSDGVTEDNVLRMMSKVRRFLVPCVLEVSAIEAIVPGFDLYFIPSVLNSKNADWIVGMHQKAMKEYGELMSMEEIVAEGYCIANPDCKAAALTEADADLNMDDIVAYARVSELLQLPIFYLEYSGVLGDIEAVKKTKAVLETSTLFYGGGIKDAETAKQYAEHADVIVVGNAVYEDFDRALKTVAAVKGE 228
               SCOP domains d3vzyb_ B: PcrB protein homolog YerE                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.eeeee......hhhhhhhhhh....eeeeee....hhhhhhhhhhhhh.....eeeee.hhhhh.....eeeeeee....hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee....hhhhhhhh.....hhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhh...eeeee....hhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vzy B   1 MYDVTEWKHVFKLDPNKDLPDEQLEILCESGTDAVIIGGSDGVTEDNVLRMMSKVRRFLVPCVLEVSAIEAIVPGFDLYFIPSVLNSKNADWIVGMHQKAMKEYGELMSMEEIVAEGYCIANPDCKAAALTEADADLNMDDIVAYARVSELLQLPIFYLEYSGVLGDIEAVKKTKAVLETSTLFYGGGIKDAETAKQYAEHADVIVVGNAVYEDFDRALKTVAAVKGE 228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   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  (0, 0)

(no "CATH Domain" information available for 3VZY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VZY)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PCRB_BACSU | O34790)
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: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.

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  3vzy
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  2.5.1.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        PCRB_BACSU | O34790: 1viz 3vzx 3vzz 3w00

(-) Related Entries Specified in the PDB File

3vzx 3vzz 3w00 3w01 3w02