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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF ALPHA-D-GLUCOSE-1-PHOSPHATE CYTIDYLYLTRANSFERASE FROM SALMONELLA TYPHI
 
Authors :  N. M. Koropatkin, H. M. Holden
Date :  09 Jul 04  (Deposition) - 07 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Nucleotidyltransferase; Mixed Alpha/Beta Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. M. Koropatkin, H. M. Holden
Molecular Structure Of Alpha-D-Glucose-1-Phosphate Cytidylyltransferase From Salmonella Typhi
J. Biol. Chem. V. 279 44023 2004
PubMed-ID: 15292268  |  Reference-DOI: 10.1074/JBC.M407755200

(-) Compounds

Molecule 1 - GLUCOSE-1-PHOSPHATE CYTIDYLYLTRANSFERASE
    Chains: A
    EC Number: 2.7.7.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    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
    Other Details: COMPLEXED WITH CYTIDYL-5'-PHOSPHATE-GLUCOSYL-6- PHOSPHATE
    Strain: CT18
    Synonym: ALPHA-D-GLUCOSE-1-PHOSPHATE CYTIDYLYLTRANSFERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1C5G1Ligand/Ion[CYTIDINE-5'-PHOSPHATE]-BETA-GLUCOSYL-PHOSPHORIC ACIDESTER
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1C5G6Ligand/Ion[CYTIDINE-5'-PHOSPHATE]-BETA-GLUCOSYL-PHOSPHORIC ACIDESTER
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:131 , ASP A:236 , C5G A:401 , HOH A:663 , HOH A:664BINDING SITE FOR RESIDUE MG A 403
2AC2SOFTWARELEU A:8 , ALA A:9 , GLY A:10 , GLY A:11 , LYS A:25 , PRO A:26 , SER A:106 , ARG A:111 , TYR A:129 , GLY A:130 , ASP A:131 , PHE A:163 , GLY A:164 , GLU A:178 , LYS A:179 , ASN A:188 , GLU A:210 , TRP A:232 , ASP A:236 , MG A:403 , HOH A:523 , HOH A:613 , HOH A:663 , HOH A:664BINDING SITE FOR RESIDUE C5G A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1TZF)

(-) 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:251
 aligned with RFBF_SALTI | Q8Z5I4 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:259
                              1                                                                                                                                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248         
           RFBF_SALTI     - --MKAVILAGGLGTRLSEETIVKPKPMVEIGGKPILWHIMKMYSVHGIKDFIICCGYKGYVIKEYFANYFLHMSDVTFHMAENRMEVHHKRVEPWNVTLVDTGDSSMTGGRLKRVAEYVKDDEAFLFTYGDGVADLDIKATIDFHKAHGKKATLTATFPPGRFGALDIQAGQVRSFQEKPKGDGAMINGGFFVLNPSVIDLIDNDATTWEQEPLMTLAQQGELMAFEHPGFWQPMDTLRDKVYLEGLWEKGKAPWKTWE 257
               SCOP domains d1tzfa_ A: Gl        ucose-1-phosphate cytidylyltransferase RfbF                                                                                                                                                                                                    SCOP domains
               CATH domains 1tzfA00 A:1-2        59 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                CATH domains
               Pfam domains ---NTP_transf        erase-1tzfA01 A:4-225                                                                                                                                                                                       ---------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....--------..hhhh.ee..eehhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhh.eeeehhhheeee........eeeeee.....hhhhhhhhhhhhh.....eeeee..eee..hhhhhhhhhhhhh..eeeeee......eeeeee..eeeeeee........ee...eee.hhhhhhh........hhhhhhhhhh..eeeeee...eee..hhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tzf A   1 MASKAVILAGGLG--------VKPKPMVEIGGKPILWHIMKMYSVHGIKDFIICCGYKGYVIKEYFANYFLHMSDVTFHMAENRMEVHHKRVEPWNVTLVDTGDSSMTGGRLKRVAEYVKDDEAFLFTYGDGVADLDIKATIDFHKAHGKKATLTATFPPGRFGALDIQAGQVRSFQEKPKGDGAMINGGFFVLNPSVIDLIDNDATTWEQEPLMTLAQQGELMAFEHPGFWQPMDTLRDKVYLEGLWEKGKAPWKTWE 259
                                    10  |      - |      30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250         
                                       13       22                                                                                                                                                                                                                                             


Chain A from PDB  Type:PROTEIN  Length:251
 aligned with RFBF_SALTY | P26396 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:259
                              1                                                                                                                                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248         
           RFBF_SALTY     - --MKAVILAGGLGTRLSEETIVKPKPMVEIGGKPILWHIMKMYSVHGIKDFIICCGYKGYVIKEYFANYFLHMSDVTFHMAENRMEVHHKRVEPWNVTLVDTGDSSMTGGRLKRVAEYVKDDEAFLFTYGDGVADLDIKATIDFHKAHGKKATLTATFPPGRFGALDIRAGQVRSFQEKPKGDGAMINGGFFVLNPSVIDLIDNDATTWEQEPLMTLAQQGELMAFEHPGFWQPMDTLRDKVYLEGLWEKGKAPWKTWE 257
               SCOP domains d1tzfa_ A: Gl        ucose-1-phosphate cytidylyltransferase RfbF                                                                                                                                                                                                    SCOP domains
               CATH domains 1tzfA00 A:1-2        59 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                CATH domains
               Pfam domains ---NTP_transf        erase-1tzfA01 A:4-225                                                                                                                                                                                       ---------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....--------..hhhh.ee..eehhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhh.eeeehhhheeee........eeeeee.....hhhhhhhhhhhhh.....eeeee..eee..hhhhhhhhhhhhh..eeeeee......eeeeee..eeeeeee........ee...eee.hhhhhhh........hhhhhhhhhh..eeeeee...eee..hhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tzf A   1 MASKAVILAGGLG--------VKPKPMVEIGGKPILWHIMKMYSVHGIKDFIICCGYKGYVIKEYFANYFLHMSDVTFHMAENRMEVHHKRVEPWNVTLVDTGDSSMTGGRLKRVAEYVKDDEAFLFTYGDGVADLDIKATIDFHKAHGKKATLTATFPPGRFGALDIQAGQVRSFQEKPKGDGAMINGGFFVLNPSVIDLIDNDATTWEQEPLMTLAQQGELMAFEHPGFWQPMDTLRDKVYLEGLWEKGKAPWKTWE 259
                                    10  |      - |      30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250         
                                       13       22
   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  (1, 1)

Asymmetric Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (8, 16)

Asymmetric Unit(hide GO term definitions)
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.

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.

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