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(-) Description

Title :  CRYSTAL STRUCTURE OF CTP:GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE FROM STAPHYLOCOCCUS AUREUS
 
Authors :  D. H. Fong, V. C. -N. Yim, M. A. D'Elia, E. D. Brown, A. M. Berghuis
Date :  04 Oct 05  (Deposition) - 27 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Cytidylyltransferase, Rossmann Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Fong, V. C. -N. Yim, M. A. D'Elia, E. D. Brown, A. M. Berghuis
Crystal Structure Of Ctp:Glycerol-3-Phosphate Cytidylyltransferase From Staphylococcus Aureus: Examination Of Structural Basis For Kinetic Mechanism.
Biochim. Biophys. Acta V. 1764 63 2006
PubMed-ID: 16344011  |  Reference-DOI: 10.1016/J.BBAPAP.2005.10.015
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.7.7.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI STR. K12 SUBSTR. W3110
    Expression System Plasmid: PKK223
    Expression System Strain: W3110
    Expression System Taxid: 316407
    Expression System Vector Type: PLASMID
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: GCT, CDP-GLYCEROL PYROPHOSPHORYLASE, TEICHOIC ACID BIOSYNTHESIS PROTEIN D

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2B7L)

(-) Sites  (0, 0)

(no "Site" information available for 2B7L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B7L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B7L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B7L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B7L)

(-) Exons   (0, 0)

(no "Exon" information available for 2B7L)

(-) 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:115
 aligned with O05155_STAAU | O05155 from UniProtKB/TrEMBL  Length:132

    Alignment length:115
                                    10        20        30        40        50        60        70        80        90       100       110     
        O05155_STAAU      1 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKRTE  115
               SCOP domains d2b7la_ A: automated matches                                                                                        SCOP domains
               CATH domains 2b7lA00 A:1-115 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh..eeeeeeehhhhhhhh......hhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeehhhhh..hhhhh...eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                2b7l A    1 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKRTE  115
                                    10        20        30        40        50        60        70        80        90       100       110     


Chain A from PDB  Type:PROTEIN  Length:115
 aligned with TARD_STAA8 | Q2G2X2 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:115
                                    10        20        30        40        50        60        70        80        90       100       110     
          TARD_STAA8      1 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKRTE  115
               SCOP domains d2b7la_ A: automated matches                                                                                        SCOP domains
               CATH domains 2b7lA00 A:1-115 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh..eeeeeeehhhhhhhh......hhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeehhhhh..hhhhh...eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                2b7l A    1 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKRTE  115
                                    10        20        30        40        50        60        70        80        90       100       110     


Chain B from PDB  Type:PROTEIN  Length:113
 aligned with O05155_STAAU | O05155 from UniProtKB/TrEMBL  Length:132

    Alignment length:113
                                    10        20        30        40        50        60        70        80        90       100       110   
        O05155_STAAU      1 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKR  113
               SCOP domains d2b7lb_ B: automated matches                                                                                      SCOP domains
               CATH domains 2b7lB00 B:501-613 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh..eeeeeeehhhhhhhh......hhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeehhhhh..hhhhh...eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                2b7l B  501 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKR  613
                                   510       520       530       540       550       560       570       580       590       600       610   


Chain B from PDB  Type:PROTEIN  Length:113
 aligned with TARD_STAA8 | Q2G2X2 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:113
                                    10        20        30        40        50        60        70        80        90       100       110   
          TARD_STAA8      1 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKR  113
               SCOP domains d2b7lb_ B: automated matches                                                                                      SCOP domains
               CATH domains 2b7lB00 B:501-613 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh..eeeeeeehhhhhhhh......hhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeehhhhh..hhhhh...eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                2b7l B  501 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKR  613
                                   510       520       530       540       550       560       570       580       590       600       610   


Chain C from PDB  Type:PROTEIN  Length:113
 aligned with O05155_STAAU | O05155 from UniProtKB/TrEMBL  Length:132

    Alignment length:113
                                    10        20        30        40        50        60        70        80        90       100       110   
        O05155_STAAU      1 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKR  113
               SCOP domains d2b7lc_ C: automated matches                                                                                      SCOP domains
               CATH domains 2b7lC00 C:1001-1113 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh..eeeeeeehhhhhhhh......hhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeehhhhh..hhhhh...eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                2b7l C 1001 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKR 1113
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110   


Chain C from PDB  Type:PROTEIN  Length:113
 aligned with TARD_STAA8 | Q2G2X2 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:113
                                    10        20        30        40        50        60        70        80        90       100       110   
          TARD_STAA8      1 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKR  113
               SCOP domains d2b7lc_ C: automated matches                                                                                      SCOP domains
               CATH domains 2b7lC00 C:1001-1113 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh..eeeeeeehhhhhhhh......hhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeehhhhh..hhhhh...eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                2b7l C 1001 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKR 1113
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110   


Chain D from PDB  Type:PROTEIN  Length:113
 aligned with O05155_STAAU | O05155 from UniProtKB/TrEMBL  Length:132

    Alignment length:113
                                    10        20        30        40        50        60        70        80        90       100       110   
        O05155_STAAU      1 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKR  113
               SCOP domains d2b7ld_ D: automated matches                                                                                      SCOP domains
               CATH domains 2b7lD00 D:1501-1613 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh..eeeeeeehhhhhhhh......hhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeehhhhh..hhhhh...eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                2b7l D 1501 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKR 1613
                                  1510      1520      1530      1540      1550      1560      1570      1580      1590      1600      1610   


Chain D from PDB  Type:PROTEIN  Length:113
 aligned with TARD_STAA8 | Q2G2X2 from UniProtKB/Swiss-Prot  Length:132

    Alignment length:113
                                    10        20        30        40        50        60        70        80        90       100       110   
          TARD_STAA8      1 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKR  113
               SCOP domains d2b7ld_ D: automated matches                                                                                      SCOP domains
               CATH domains 2b7lD00 D:1501-1613 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh..eeeeeeehhhhhhhh......hhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeeehhhhh..hhhhh...eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                2b7l D 1501 MKRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIPEKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKR 1613
                                  1510      1520      1530      1540      1550      1560      1570      1580      1590      1600      1610
   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, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B7L)

(-) Gene Ontology  (8, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O05155_STAAU | O05155)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0047348    glycerol-3-phosphate cytidylyltransferase activity    Catalysis of the reaction: sn-glycerol 3-phosphate + CTP = CDP-glycerol + diphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0019350    teichoic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of teichoic acid, any polymer occurring in the cell wall, membrane or capsule of Gram-positive bacteria and containing chains of glycerol phosphate or ribitol phosphate residues.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B,C,D   (TARD_STAA8 | Q2G2X2)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0047348    glycerol-3-phosphate cytidylyltransferase activity    Catalysis of the reaction: sn-glycerol 3-phosphate + CTP = CDP-glycerol + diphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    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:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0019350    teichoic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of teichoic acid, any polymer occurring in the cell wall, membrane or capsule of Gram-positive bacteria and containing chains of glycerol phosphate or ribitol phosphate residues.
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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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1coz CTP-BOUND CTP:GLYCEROL-3-CYTIDYLYLTRANSFERASE FROM BACILLUS SUBTILLIS
1n1d GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE COMPLEXED WITH CDP-GLYCEROL