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(-) Description

Title :  ALPHA-D-GLUCOSE-1-PHOSPHATE CYTIDYLYLTRANSFERASE COMPLEXED WITH CTP
 
Authors :  N. M. Koropatkin, W. W. Cleland, H. M. Holden
Date :  14 Dec 04  (Deposition) - 11 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Cdp-Glucose Pyrophosphorylase, Nucleotidyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. M. Koropatkin, W. W. Cleland, H. M. Holden
Kinetic And Structural Analysis Of Alpha-D-Glucose-1-Phosphate Cytidylyltransferase From Salmonella Typhi.
J. Biol. Chem. V. 280 10774 2005
PubMed-ID: 15634670  |  Reference-DOI: 10.1074/JBC.M414111200

(-) Compounds

Molecule 1 - GLUCOSE-1-PHOSPHATE CYTIDYLYLTRANSFERASE
    Chains: A
    EC Number: 2.7.7.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RFBF
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHI
    Organism Taxid: 220341
    Strain: CT18
    Synonym: ALPHA-D-GLUCOSE-1-PHOSPHATE CYTIDYLYLTRANSFERASE, CDP- GLUCOSE PYROPHOSPHORYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CTP1Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CTP6Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:15 , ASP A:131 , ASP A:236 , CTP A:401BINDING SITE FOR RESIDUE MG A 402
2AC2SOFTWAREHIS A:79BINDING SITE FOR RESIDUE NI A 403
3AC3SOFTWARECTP A:401BINDING SITE FOR RESIDUE MG A 501
4AC4SOFTWARELEU A:8 , ALA A:9 , GLY A:10 , GLY A:11 , LEU A:12 , GLY A:13 , THR A:14 , ARG A:15 , LYS A:25 , SER A:106 , MET A:107 , ARG A:111 , GLY A:130 , ASP A:131 , ASP A:236 , MG A:402 , MG A:501 , HOH A:1701 , HOH A:1907 , HOH A:2513 , HOH A:2515BINDING SITE FOR RESIDUE CTP A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WVC)

(-) 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:254
 aligned with RFBF_SALTI | Q8Z5I4 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:258
                             1                                                                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249        
           RFBF_SALTI     - -MKAVILAGGLGTRLSEETIVKPKPMVEIGGKPILWHIMKMYSVHGIKDFIICCGYKGYVIKEYFANYFLHMSDVTFHMAENRMEVHHKRVEPWNVTLVDTGDSSMTGGRLKRVAEYVKDDEAFLFTYGDGVADLDIKATIDFHKAHGKKATLTATFPPGRFGALDIQAGQVRSFQEKPKGDGAMINGGFFVLNPSVIDLIDNDATTWEQEPLMTLAQQGELMAFEHPGFWQPMDTLRDKVYLEGLWEKGKAPWKTWE 257
               SCOP domains d1wvca_ A: Glucose-1-phosphate cytidylyltransferase RfbF                                                                                                                                                                                                           SCOP domains
               CATH domains 1wvcA00 A:2-259 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhh..hhhh.ee..eehhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhh.eeeehhhheeee........eeeeee.....hhhhhhhhhhhhhh....eeeee..eee..hhhhhhhhhhhhh..eeeeee.....-..eeee..eeeee.---......ee...eee.hhhhhhh.........hhhhhhhhh..eeeeee...eee..hhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wvc A   2 ASKAVILAGGLGTRLSEETIVKPKPMVEIGGKPILWHIMKMYSVHGIKDFIICCGYKGYVIKEYFANYFLHMSDVTFHMAENRMEVHHKRVEPWNVTLVDTGDSSMTGGRLKRVAEYVKDDEAFLFTYGDGVADLDIKATIDFHKAHGKKATLTATFPPGR-GALDIQAGQVRSFQ---KGDGAMINGGFFVLNPSVIDLIDNDATTWEQEPLMTLAQQGELMAFEHPGFWQPMDTLRDKVYLEGLWEKGKAPWKTWE 259
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161| |    171     | 181       191       201       211       221       231       241       251        
                                                                                                                                                                                          162 |          177 181                                                                              
                                                                                                                                                                                            164                                                                                               


Chain A from PDB  Type:PROTEIN  Length:254
 aligned with RFBF_SALTY | P26396 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:258
                             1                                                                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249        
           RFBF_SALTY     - -MKAVILAGGLGTRLSEETIVKPKPMVEIGGKPILWHIMKMYSVHGIKDFIICCGYKGYVIKEYFANYFLHMSDVTFHMAENRMEVHHKRVEPWNVTLVDTGDSSMTGGRLKRVAEYVKDDEAFLFTYGDGVADLDIKATIDFHKAHGKKATLTATFPPGRFGALDIRAGQVRSFQEKPKGDGAMINGGFFVLNPSVIDLIDNDATTWEQEPLMTLAQQGELMAFEHPGFWQPMDTLRDKVYLEGLWEKGKAPWKTWE 257
               SCOP domains d1wvca_ A: Glucose-1-phosphate cytidylyltransferase RfbF                                                                                                                                                                                                           SCOP domains
               CATH domains 1wvcA00 A:2-259 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee....hhhhhhhhh..hhhh.ee..eehhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhh.eeeehhhheeee........eeeeee.....hhhhhhhhhhhhhh....eeeee..eee..hhhhhhhhhhhhh..eeeeee.....-..eeee..eeeee.---......ee...eee.hhhhhhh.........hhhhhhhhh..eeeeee...eee..hhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wvc A   2 ASKAVILAGGLGTRLSEETIVKPKPMVEIGGKPILWHIMKMYSVHGIKDFIICCGYKGYVIKEYFANYFLHMSDVTFHMAENRMEVHHKRVEPWNVTLVDTGDSSMTGGRLKRVAEYVKDDEAFLFTYGDGVADLDIKATIDFHKAHGKKATLTATFPPGR-GALDIQAGQVRSFQ---KGDGAMINGGFFVLNPSVIDLIDNDATTWEQEPLMTLAQQGELMAFEHPGFWQPMDTLRDKVYLEGLWEKGKAPWKTWE 259
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161| |    171     | 181       191       201       211       221       231       241       251        
                                                                                                                                                                                          162 |          177 181                                                                              
                                                                                                                                                                                            164
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1WVC)

(-) Gene Ontology  (8, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (RFBF_SALTY | P26396)
molecular function
    GO:0047343    glucose-1-phosphate cytidylyltransferase activity    Catalysis of the reaction: alpha-D-glucose 1-phosphate + CTP = CDP-D-glucose + diphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0009243    O antigen biosynthetic process    The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.
    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:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

Chain A   (RFBF_SALTI | Q8Z5I4)
molecular function
    GO:0047343    glucose-1-phosphate cytidylyltransferase activity    Catalysis of the reaction: alpha-D-glucose 1-phosphate + CTP = CDP-D-glucose + diphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0009243    O antigen biosynthetic process    The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.
    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:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

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 Related Entries

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

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        RFBF_SALTI | Q8Z5I4: 1tzf
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(-) Related Entries Specified in the PDB File

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