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(-) Description

Title :  CRYSTAL STRUCTURE OF CYTIDYLYLTRANSFERASE FROM VIBRIO CHOLERAE
 
Authors :  J. Hattne, D. Borek, S. Grimshaw, C. Nakka, R. Rostankowski, Z. Otwinow Center For Structural Genomics Of Infectious Diseases (Csgi
Date :  05 Aug 10  (Deposition) - 22 Sep 10  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Center For Structural Genomics Of Infectious Diseases, Csgid, Cytidylyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Hattne, D. Borek, S. Grimshaw, C. Nakka, R. Rostankowski, Z. Otwinowski, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Cytidylyltransferase From Vibrio Cholerae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.7.7.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)-MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: BACTERIAL PLASMID
    Fragment: 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
    Gene: KDSB, VC1875, VC_1875
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR
    Organism Taxid: 243277
    Strain: N16961
    Synonym: CMP-2-KETO-3-DEOXYOCTULOSONIC ACID SYNTHASE, CMP-KDO SYNTHASE, CKS

 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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:249 , GLN A:252 , HOH A:301 , HOH A:413 , SER B:120 , ALA D:117BINDING SITE FOR RESIDUE NA A 253

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OAM)

(-) 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:252
 aligned with KDSB_VIBCH | Q9KQX2 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  
           KDSB_VIBCH     1 MSFTVVIPARYQSTRLPGKPLADIGGKPMIQWVYEQAMQAGADRVIIATDDERVEQAVQAFGGVVCMTSPNHQSGTERLAEVVAKMAIPADHIVVNVQGDEPLIPPAIIRQVADNLAACSAPMATLAVEIEDEAEVFNPNAVKVITDKSGYALYFSRATIPWDRDNFAKADKAIVQPLLRHIGIYAYRAGFINTYLDWQPSQLEKIECLEQLRVLWHGEKIHVAVALEAPPAGVDTPEDLEVVRRIVAERAQ 252
               SCOP domains d3oama_ A: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.........hhhh.ee..eehhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee......hhhhhhhhhhhhh......eeee........hhhhhhhhhhhhhhh...eeeeeeee.hhhhhh.....eeee.....eeeee......hhhhhhh........eeeeeeeeeee.hhhhhhhhh..hhhhhhhh..hhhhhhh...eeeee..........hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oam A   1 MSFTVVIPARYQSTRLPGKPLADIGGKPMIQWVYEQAMQAGADRVIIATDDERVEQAVQAFGGVVCMTSPNHQSGTERLAEVVAKMAIPADHIVVNVQGDEPLIPPAIIRQVADNLAACSAPMATLAVEIEDEAEVFNPNAVKVITDKSGYALYFSRATIPWDRDNFAKADKAIVQPLLRHIGIYAYRAGFINTYLDWQPSQLEKIECLEQLRVLWHGEKIHVAVALEAPPAGVDTPEDLEVVRRIVAERAQ 252
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  


Chain B from PDB  Type:PROTEIN  Length:251
 aligned with KDSB_VIBCH | Q9KQX2 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 
           KDSB_VIBCH     1 MSFTVVIPARYQSTRLPGKPLADIGGKPMIQWVYEQAMQAGADRVIIATDDERVEQAVQAFGGVVCMTSPNHQSGTERLAEVVAKMAIPADHIVVNVQGDEPLIPPAIIRQVADNLAACSAPMATLAVEIEDEAEVFNPNAVKVITDKSGYALYFSRATIPWDRDNFAKADKAIVQPLLRHIGIYAYRAGFINTYLDWQPSQLEKIECLEQLRVLWHGEKIHVAVALEAPPAGVDTPEDLEVVRRIVAERA 251
               SCOP domains d3oamb_ B: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhh.ee..eehhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee......hhhhhhhhhhhhh......eeee........hhhhhhhhhhhhhh....eeeeeeee.hhhhhh.....eeee.....eeeee.....................eeeeeeeeeeehhhhhhhhhh..hhhhhhhh..hhhhhhh...eeeee..........hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oam B   1 MSFTVVIPARYQSTRLPGKPLADIGGKPMIQWVYEQAMQAGADRVIIATDDERVEQAVQAFGGVVCMTSPNHQSGTERLAEVVAKMAIPADHIVVNVQGDEPLIPPAIIRQVADNLAACSAPMATLAVEIEDEAEVFNPNAVKVITDKSGYALYFSRATIPWDRDNFAKADKAIVQPLLRHIGIYAYRAGFINTYLDWQPSQLEKIECLEQLRVLWHGEKIHVAVALEAPPAGVDTPEDLEVVRRIVAERA 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 


Chain C from PDB  Type:PROTEIN  Length:251
 aligned with KDSB_VIBCH | Q9KQX2 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 
           KDSB_VIBCH     1 MSFTVVIPARYQSTRLPGKPLADIGGKPMIQWVYEQAMQAGADRVIIATDDERVEQAVQAFGGVVCMTSPNHQSGTERLAEVVAKMAIPADHIVVNVQGDEPLIPPAIIRQVADNLAACSAPMATLAVEIEDEAEVFNPNAVKVITDKSGYALYFSRATIPWDRDNFAKADKAIVQPLLRHIGIYAYRAGFINTYLDWQPSQLEKIECLEQLRVLWHGEKIHVAVALEAPPAGVDTPEDLEVVRRIVAERA 251
               SCOP domains d3oamc_ C: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.........hhhh.ee..eehhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee......hhhhhhhhhhhhh......eeee........hhhhhhhhhhhhhhh...eeeeeeee.hhhhhh.....eeee.....eeeee......hhhhhh.........eeeeeeeeeeehhhhhhhhhh..hhhhhhhh..hhhhhhh...eeeee..........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oam C   1 MSFTVVIPARYQSTRLPGKPLADIGGKPMIQWVYEQAMQAGADRVIIATDDERVEQAVQAFGGVVCMTSPNHQSGTERLAEVVAKMAIPADHIVVNVQGDEPLIPPAIIRQVADNLAACSAPMATLAVEIEDEAEVFNPNAVKVITDKSGYALYFSRATIPWDRDNFAKADKAIVQPLLRHIGIYAYRAGFINTYLDWQPSQLEKIECLEQLRVLWHGEKIHVAVALEAPPAGVDTPEDLEVVRRIVAERA 251
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250 


Chain D from PDB  Type:PROTEIN  Length:250
 aligned with KDSB_VIBCH | Q9KQX2 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
           KDSB_VIBCH     1 MSFTVVIPARYQSTRLPGKPLADIGGKPMIQWVYEQAMQAGADRVIIATDDERVEQAVQAFGGVVCMTSPNHQSGTERLAEVVAKMAIPADHIVVNVQGDEPLIPPAIIRQVADNLAACSAPMATLAVEIEDEAEVFNPNAVKVITDKSGYALYFSRATIPWDRDNFAKADKAIVQPLLRHIGIYAYRAGFINTYLDWQPSQLEKIECLEQLRVLWHGEKIHVAVALEAPPAGVDTPEDLEVVRRIVAER 250
               SCOP domains d3oamd_ D: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---CTP_transf_3-3oamD01 D:4-221                                                                                                                                                                                              ----------------------------- Pfam domains (1)
           Pfam domains (2) ---CTP_transf_3-3oamD02 D:4-221                                                                                                                                                                                              ----------------------------- Pfam domains (2)
           Pfam domains (3) ---CTP_transf_3-3oamD03 D:4-221                                                                                                                                                                                              ----------------------------- Pfam domains (3)
           Pfam domains (4) ---CTP_transf_3-3oamD04 D:4-221                                                                                                                                                                                              ----------------------------- Pfam domains (4)
         Sec.struct. author ..eeeeeee........hhhh.ee..eehhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee.......hhhhhhhhhhhh......eeee........hhhhhhhhhhhhhh....eeeeeeee.hhhhhh.....eeee.....eeeee......hhhhhh.........eeeeeeeeeee.hhhhhhhhh..hhhhhhhh..hhhhhhh...eeeee..........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oam D   1 MSFTVVIPARYQSTRLPGKPLADIGGKPMIQWVYEQAMQAGADRVIIATDDERVEQAVQAFGGVVCMTSPNHQSGTERLAEVVAKMAIPADHIVVNVQGDEPLIPPAIIRQVADNLAACSAPMATLAVEIEDEAEVFNPNAVKVITDKSGYALYFSRATIPWDRDNFAKADKAIVQPLLRHIGIYAYRAGFINTYLDWQPSQLEKIECLEQLRVLWHGEKIHVAVALEAPPAGVDTPEDLEVVRRIVAER 250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (KDSB_VIBCH | Q9KQX2)
molecular function
    GO:0008690    3-deoxy-manno-octulosonate cytidylyltransferase activity    Catalysis of the reaction: CTP + 3-deoxy-D-manno-octulosonate = diphosphate + CMP-3-deoxy-D-manno-octulosonate.
    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:0033468    CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of CMP-keto-3-deoxy-D-manno-octulosonic acid, a substance composed of the acidic sugar 3-deoxy-D-manno-octulosonic acid in glycosidic linkage with cytidine monophosphate.
    GO:0019294    keto-3-deoxy-D-manno-octulosonic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of keto-3-deoxy-D-manno-octulosonic acid, an acidic sugar present in lipopolysaccharides of the outer membranes of some Gram-negative bacteria.
    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.
    GO:0009244    lipopolysaccharide core region biosynthetic process    The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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