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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI LIPOPOLYSACCHARIDE SPECIFIC CMP-KDO SYNTHETASE
 
Authors :  D. J. Heyes, C. W. Levy, P. Lafite, N. S. Scrutton, D. Leys
Date :  14 Oct 09  (Deposition) - 10 Nov 09  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Kdsb Synthetase Deoxy Kdo Complex, Lipopolysaccharide Biosynthesis, Magnesium, Nucleotidyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Heyes, C. Levy, P. Lafite, I. S. Roberts, M. Goldrick, A. V. Stachulski, S. B. Rossington, D. Stanford, S. E. J. Rigby, N. S. Scrutton, D. Leys
Structure-Based Mechanism Of Cmp-2-Keto-3-Deoxymanno-Octulonic Acid Synthetase: Convergent Evolution Of A Sugar-Activating Enzyme With Dna/Rna Polymerases
J. Biol. Chem. V. 284 35514 2009
PubMed-ID: 19815542  |  Reference-DOI: 10.1074/JBC.M109.056630

(-) Compounds

Molecule 1 - 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
    Chains: C, D, A, B
    EC Number: 2.7.7.38
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: CMP-KDO SYNTHETASE, CMP-2-KETO-3-DEOXYOCTULOSONIC ACID SYNTHETASE, CKS

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3K8E)

(-) Sites  (0, 0)

(no "Site" information available for 3K8E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K8E)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ile C:160 -Pro C:161
2Ile D:160 -Pro D:161
3Phe D:167 -Ala D:168
4Ile A:160 -Pro A:161
5Ile B:160 -Pro B:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K8E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K8E)

(-) Exons   (0, 0)

(no "Exon" information available for 3K8E)

(-) 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:242
 aligned with KDSB_ECOLI | P04951 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     
           KDSB_ECOLI     2 SFVVIIPARYASTRLPGKPLVDINGKPMIVHVLERARESGAERIIVATDHEDVARAVEAAGGEVCMTRADHQSGTERLAEVVEKCAFSDDTVIVNVQGDEPMIPATIIRQVADNLAQRQVGMATLAVPIHNAEEAFNPNAVKVVLDAEGYALYFSRATIPWDRDRFAEGLETVGDNFLRHLGIYGYRAGFIRRYVNWQPSPLEHIEMLEQLRVLWYGEKIHVAVAQEVPGTGVDTPEDLERVRAE 246
               SCOP domains d3k8ea_ A: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains 3k8eA00 A:2-246 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........hhhh.ee..eehhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee......hhhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhh....eeeeeee..hhhhhh.....eeee.....eeeee..............---.....eeeeeeeeeehhhhhhhhhh..hhhhhhhh..hhhhhhh...eeeee..........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k8e A   2 SFVVIIPARYASTRLPGKPLVDINGKPMIVHVLERARESGAERIIVATDHEDVARAVEAAGGEVCMTRADHQSGTERLAEVVEKCAFSDDTVIVNVQGDEPMIPATIIRQVADNLAQRQVGMATLAVPIHNAEEAFNPNAVKVVLDAEGYALYFSRATIPWDRDRFAEG---VGDNFLRHLGIYGYRAGFIRRYVNWQPSPLEHIEMLEQLRVLWYGEKIHVAVAQEVPGTGVDTPEDLERVRAE 246
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        |-  |    181       191       201       211       221       231       241     
                                                                                                                                                                                                  170 174                                                                        


Chain B from PDB  Type:PROTEIN  Length:246
 aligned with KDSB_ECOLI | P04951 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:246
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      
           KDSB_ECOLI     2 SFVVIIPARYASTRLPGKPLVDINGKPMIVHVLERARESGAERIIVATDHEDVARAVEAAGGEVCMTRADHQSGTERLAEVVEKCAFSDDTVIVNVQGDEPMIPATIIRQVADNLAQRQVGMATLAVPIHNAEEAFNPNAVKVVLDAEGYALYFSRATIPWDRDRFAEGLETVGDNFLRHLGIYGYRAGFIRRYVNWQPSPLEHIEMLEQLRVLWYGEKIHVAVAQEVPGTGVDTPEDLERVRAEM 247
               SCOP domains d3k8eb_ B: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains 3k8eB00 B:2-247 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.........hhhh.ee..eehhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee......hhhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhh....eeeeeee..hhhhhh.....eeee.....eeeee......hhhhhhhh........eeeeeeeeeehhhhhhhh....hhhhhhhh..hhhhhhh...eeeee..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k8e B   2 SFVVIIPARYASTRLPGKPLVDINGKPMIVHVLERARESGAERIIVATDHEDVARAVEAAGGEVCMTRADHQSGTERLAEVVEKCAFSDDTVIVNVQGDEPMIPATIIRQVADNLAQRQVGMATLAVPIHNAEEAFNPNAVKVVLDAEGYALYFSRATIPWDRDRFAEGLETVGDNFLRHLGIYGYRAGFIRRYVNWQPSPLEHIEMLEQLRVLWYGEKIHVAVAQEVPGTGVDTPEDLERVRAEM 247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      


Chain C from PDB  Type:PROTEIN  Length:244
 aligned with KDSB_ECOLI | P04951 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    
           KDSB_ECOLI     2 SFVVIIPARYASTRLPGKPLVDINGKPMIVHVLERARESGAERIIVATDHEDVARAVEAAGGEVCMTRADHQSGTERLAEVVEKCAFSDDTVIVNVQGDEPMIPATIIRQVADNLAQRQVGMATLAVPIHNAEEAFNPNAVKVVLDAEGYALYFSRATIPWDRDRFAEGLETVGDNFLRHLGIYGYRAGFIRRYVNWQPSPLEHIEMLEQLRVLWYGEKIHVAVAQEVPGTGVDTPEDLERVRA 245
               SCOP domains d3k8ec_ C: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains 3k8eC00 C:2-245 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........hhhhh.....hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee......hhhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhh...eeeeeee..hhhhhh.....eeee.....eeeee......hhhhhhhh........eeeeeeeeeehhhhhhhh....hhhhhhhh..hhhhhhh...eeeee..........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k8e C   2 SFVVIIPARYASTRLPGKPLVDINGKPMIVHVLERARESGAERIIVATDHEDVARAVEAAGGEVCMTRADHQSGTERLAEVVEKCAFSDDTVIVNVQGDEPMIPATIIRQVADNLAQRQVGMATLAVPIHNAEEAFNPNAVKVVLDAEGYALYFSRATIPWDRDRFAEGLETVGDNFLRHLGIYGYRAGFIRRYVNWQPSPLEHIEMLEQLRVLWYGEKIHVAVAQEVPGTGVDTPEDLERVRA 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    


Chain D from PDB  Type:PROTEIN  Length:238
 aligned with KDSB_ECOLI | P04951 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:245
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242     
           KDSB_ECOLI     3 FVVIIPARYASTRLPGKPLVDINGKPMIVHVLERARESGAERIIVATDHEDVARAVEAAGGEVCMTRADHQSGTERLAEVVEKCAFSDDTVIVNVQGDEPMIPATIIRQVADNLAQRQVGMATLAVPIHNAEEAFNPNAVKVVLDAEGYALYFSRATIPWDRDRFAEGLETVGDNFLRHLGIYGYRAGFIRRYVNWQPSPLEHIEMLEQLRVLWYGEKIHVAVAQEVPGTGVDTPEDLERVRAEM 247
               SCOP domains d3k8ed_ D: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains 3k8eD00 D:3-247 Spore Coat Polysaccharide Biosynthesis Protein SpsA    ; Chain A                                                                                                                                                                      CATH domains
           Pfam domains (1) -CTP_transf_3-3k8eD01 D:4-221                                                                                                                                                                                              -------------------------- Pfam domains (1)
           Pfam domains (2) -CTP_transf_3-3k8eD02 D:4-221                                                                                                                                                                                              -------------------------- Pfam domains (2)
           Pfam domains (3) -CTP_transf_3-3k8eD03 D:4-221                                                                                                                                                                                              -------------------------- Pfam domains (3)
           Pfam domains (4) -CTP_transf_3-3k8eD04 D:4-221                                                                                                                                                                                              -------------------------- Pfam domains (4)
         Sec.struct. author .eeeee.........hhhh.ee..eehhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee..----.hhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhh...eeeeeee..hhhhhh.....eeee.....eeeee..............---.....eeeeeeeeeehhhhhhhh....hhhhhhhh..hhhhhhh...eeeee..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k8e D   3 FVVIIPARYASTRLPGKPLVDINGKPMIVHVLERARESGAERIIVATDHEDVARAVEAAGGEVCMTR----SGTERLAEVVEKCAFSDDTVIVNVQGDEPMIPATIIRQVADNLAQRQVGMATLAVPIHNAEEAFNPNAVKVVLDAEGYALYFSRATIPWDRDRFAEG---VGDNFLRHLGIYGYRAGFIRRYVNWQPSPLEHIEMLEQLRVLWYGEKIHVAVAQEVPGTGVDTPEDLERVRAEM 247
                                    12        22        32        42        52        62      |  - |      82        92       102       112       122       132       142       152       162       | - |     182       192       202       212       222       232       242     
                                                                                             69   74                                                                                             170 174
   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  (1, 4)

Asymmetric Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (KDSB_ECOLI | P04951)
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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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.
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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  Cis Peptide Bonds
    Ile A:160 - Pro A:161   [ RasMol ]  
    Ile B:160 - Pro B:161   [ RasMol ]  
    Ile C:160 - Pro C:161   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        KDSB_ECOLI | P04951: 1vh1 3k8d

(-) Related Entries Specified in the PDB File

3k8d