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(-) Description

Title :  GLYCEROL-3-PHOSPHATE CYTIDYLYLTRANSFERASE COMPLEXED WITH CDP-GLYCEROL
 
Authors :  K. A. Pattridge, C. H. Weber, J. A. Friesen, S. Sankar, C. Kent, M. L. Ludwig
Date :  17 Oct 02  (Deposition) - 11 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Alpha/Beta Fold, Cytidylyltransferase, Nucleotidyltransferase, Negative Cooperativity, Cdp-Glycerol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. A. Pattridge, C. H. Weber, J. A. Friesen, S. Sanker, C. Kent, M. L. Ludwig
Glycerol-3-Phosphate Cytidylyltransferase. Structural Changes Induced By Binding Of Cdp-Glycerol And The Role Of Lysine Residues In Catalysis
J. Biol. Chem. V. 278 51863 2003
PubMed-ID: 14506262  |  Reference-DOI: 10.1074/JBC.M306174200
(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
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    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  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1C2G4Ligand/Ion[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1C2G2Ligand/Ion[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1C2G2Ligand/Ion[CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER
2SO41Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:14 , HIS A:17 , ARG A:113 , SER A:118 , THR A:119 , C2G A:130 , HOH A:909BINDING SITE FOR RESIDUE SO4 A 701
2AC2SOFTWAREARG D:113 , SER D:118 , THR D:119 , THR D:120 , C2G D:430 , HOH D:820 , HOH D:881BINDING SITE FOR RESIDUE SO4 D 702
3AC3SOFTWAREHIS B:14 , HIS B:17 , SER B:118 , THR B:119 , C2G B:230 , HOH B:780BINDING SITE FOR RESIDUE SO4 B 705
4AC4SOFTWAREGLY A:8 , THR A:9 , PHE A:10 , HIS A:17 , SER A:36 , LYS A:44 , LYS A:46 , GLU A:71 , LYS A:77 , MET A:91 , GLY A:92 , ASP A:94 , TRP A:95 , ARG A:113 , THR A:114 , ILE A:117 , SO4 A:701 , HOH A:721 , HOH A:733 , HOH A:745 , HOH A:845BINDING SITE FOR RESIDUE C2G A 130
5AC5SOFTWAREGLY B:8 , THR B:9 , PHE B:10 , SER B:36 , LYS B:44 , LYS B:46 , GLU B:71 , TRP B:74 , LYS B:77 , GLY B:92 , ASP B:94 , TRP B:95 , PHE B:99 , ARG B:113 , THR B:114 , ILE B:117 , SO4 B:705 , HOH B:707 , HOH B:740 , HOH B:748 , HOH B:780BINDING SITE FOR RESIDUE C2G B 230
6AC6SOFTWARETYR C:7 , GLY C:8 , THR C:9 , PHE C:10 , HIS C:17 , SER C:36 , LYS C:44 , LYS C:46 , GLU C:71 , LYS C:77 , MET C:91 , GLY C:92 , ASP C:94 , TRP C:95 , ARG C:113 , THR C:114 , ILE C:117 , HOH C:710 , HOH C:760 , HOH C:839BINDING SITE FOR RESIDUE C2G C 330
7AC7SOFTWAREGLY D:8 , THR D:9 , PHE D:10 , SER D:36 , LYS D:44 , LYS D:46 , GLU D:71 , LYS D:77 , MET D:91 , GLY D:92 , ASP D:94 , TRP D:95 , ARG D:113 , THR D:114 , ILE D:117 , SO4 D:702 , HOH D:722 , HOH D:723 , HOH D:739 , HOH D:812 , HOH D:820 , HOH D:892BINDING SITE FOR RESIDUE C2G D 430

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N1D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N1D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N1D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N1D)

(-) Exons   (0, 0)

(no "Exon" information available for 1N1D)

(-) 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:126
 aligned with TAGD_BACSU | P27623 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
           TAGD_BACSU     1 MKKVITYGTFDLLHWGHIKLLERAKQLGDYLVVAISTDEFNLQKQKKAYHSYEHRKLILETIRYVDEVIPEKNWEQKKQDIIDHNIDVFVMGDDWEGKFDFLKDQCEVVYLPRTEGISTTKIKEEI 126
               SCOP domains d1n1da_ A: CTP:glycerol-3-phosphate cytidylyltransferase                                                                       SCOP domains
               CATH domains 1n1dA00 A:1-126 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhh...eeeeeeehhhhhhh.......hhhhhhhhhh......eeeee.hhhhhhhhhhhh...eeeee.hhh..hhhhh...eeeee......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n1d A   1 MKKVITYGTFDLLHWGHIKLLERAKQLGDYLVVAISTDEFNLQKQKKAYHSYEHRKLILETIRYVDEVIPEKNWEQKKQDIIDHNIDVFVMGDDWEGKFDFLKDQCEVVYLPRTEGISTTKIKEEI 126
                                    10        20        30        40        50        60        70        80        90       100       110       120      


Chain B from PDB  Type:PROTEIN  Length:126
 aligned with TAGD_BACSU | P27623 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
           TAGD_BACSU     1 MKKVITYGTFDLLHWGHIKLLERAKQLGDYLVVAISTDEFNLQKQKKAYHSYEHRKLILETIRYVDEVIPEKNWEQKKQDIIDHNIDVFVMGDDWEGKFDFLKDQCEVVYLPRTEGISTTKIKEEI 126
               SCOP domains d1n1db_ B: CTP:glycerol-3-phosphate cytidylyltransferase                                                                       SCOP domains
               CATH domains 1n1dB00 B:1-126 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhh...eeeeeeehhhhhhhh......hhhhhhhhhhh.....eeeee....hhhhhhhhh...eeeee.hhh..hhhhh...eeeee......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n1d B   1 MKKVITYGTFDLLHWGHIKLLERAKQLGDYLVVAISTDEFNLQKQKKAYHSYEHRKLILETIRYVDEVIPEKNWEQKKQDIIDHNIDVFVMGDDWEGKFDFLKDQCEVVYLPRTEGISTTKIKEEI 126
                                    10        20        30        40        50        60        70        80        90       100       110       120      


Chain C from PDB  Type:PROTEIN  Length:126
 aligned with TAGD_BACSU | P27623 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
           TAGD_BACSU     1 MKKVITYGTFDLLHWGHIKLLERAKQLGDYLVVAISTDEFNLQKQKKAYHSYEHRKLILETIRYVDEVIPEKNWEQKKQDIIDHNIDVFVMGDDWEGKFDFLKDQCEVVYLPRTEGISTTKIKEEI 126
               SCOP domains d1n1dc_ C: CTP:glycerol-3-phosphate cytidylyltransferase                                                                       SCOP domains
               CATH domains 1n1dC00 C:1-126 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhh...eeeeeeehhhhhhhh......hhhhhhhhhh......eeeee....hhhhhhhhh...eeeee.hhh..hhhhhhh.eeeee......hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n1d C   1 MKKVITYGTFDLLHWGHIKLLERAKQLGDYLVVAISTDEFNLQKQKKAYHSYEHRKLILETIRYVDEVIPEKNWEQKKQDIIDHNIDVFVMGDDWEGKFDFLKDQCEVVYLPRTEGISTTKIKEEI 126
                                    10        20        30        40        50        60        70        80        90       100       110       120      


Chain D from PDB  Type:PROTEIN  Length:126
 aligned with TAGD_BACSU | P27623 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
           TAGD_BACSU     1 MKKVITYGTFDLLHWGHIKLLERAKQLGDYLVVAISTDEFNLQKQKKAYHSYEHRKLILETIRYVDEVIPEKNWEQKKQDIIDHNIDVFVMGDDWEGKFDFLKDQCEVVYLPRTEGISTTKIKEEI 126
               SCOP domains d1n1dd_ D: CTP:glycerol-3-phosphate cytidylyltransferase                                                                       SCOP domains
               CATH domains 1n1dD00 D:1-126 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhh..eeeeeeehhhhhhh.......hhhhhhhhhh......eeeee.hhhhhhhhhhhh...eeeee.hhh..hhhhh...eeeee......hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n1d D   1 MKKVITYGTFDLLHWGHIKLLERAKQLGDYLVVAISTDEFNLQKQKKAYHSYEHRKLILETIRYVDEVIPEKNWEQKKQDIIDHNIDVFVMGDDWEGKFDFLKDQCEVVYLPRTEGISTTKIKEEI 126
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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 1N1D)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TAGD_BACSU | P27623)
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:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    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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  1n1d
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  TAGD_BACSU | P27623
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 Related Entries

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

UniProtKB/Swiss-Prot
        TAGD_BACSU | P27623: 1coz

(-) Related Entries Specified in the PDB File

1coz GPCT COMPLEXED WITH CTP