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(-) Description

Title :  CRYSTAL STRUCTURE OF CMP-KDO SYNTHETASE
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541
(for further references see the PDB file header)

(-) 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 Taxid: 562
    Gene: KDSB, B0918
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CMP-KDO SYNTHETASE, CMP-2-KETO-3-DEOXYOCTULOSONIC ACID SYNTHETASE, CKS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 24)

Asymmetric/Biological Unit (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1VH1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VH1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ile A:160 -Pro A:161
2Ile B:160 -Pro B:161
3Ile C:160 -Pro C:161
4Ile D:160 -Pro D:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VH1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VH1)

(-) Exons   (0, 0)

(no "Exon" information available for 1VH1)

(-) Sequences/Alignments

Asymmetric/Biological 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:239
 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 d1vh1a_ A: CM  P:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)syntheta     se                                                                                                                                                                            SCOP domains
               CATH domains 1vh1A00 A:2-2  46 Spore Coat Polysaccharide Biosynthesis Protein Sps     A; Chain A                                                                                                                                                                  - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee......--......ee..eehhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee..-----hhhhhhhhhhhh......eeee........hhhhhhhhhhhhhhh...eeeeeee..hhhhhh.....eeee.....eeeee......hhhhhh..........eeeeeeeeeehhhhhhhhhh..hhhhhhhh..hhhhhhh...eeeee..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vh1 A   2 SFVVIIPARYAST--PGKPLVDINGKPmIVHVLERARESGAERIIVATDHEDVARAVEAAGGEVCmTR-----GTERLAEVVEKCAFSDDTVIVNVQGDEPmIPATIIRQVADNLAQRQVGmATLAVPIHNAEEAFNPNAVKVVLDAEGYALYFSRATIPWDRDRFAEGLETVGDNFLRHLGIYGYRAGFIRRYVNWQPSPLEHIEmLEQLRVLWYGEKIHVAVAQEVPGTGVDTPEDLERVRAEm 247
                                    11  |  |  21       |31        41        51        61     | | -   |    81        91       101 |     111       121 |     131       141       151       161       171       181       191       201      |211       221       231       241     |
                                       14 17          29-MSE                                67-MSE  75                         103-MSE             123-MSE                                                                              208-MSE                                247-MSE
                                                                                              69                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:224
 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 d1vh1b_ B:       CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)synth     etase                                                                                                                                                                        SCOP domains
               CATH domains 1vh1B00 B:      2-246 Spore Coat Polysaccharide Biosynthesis Protein      SpsA; Chain A                                                                                                                                                              - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..------..........hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee...-----hhhhhhhhhhh......eee.........hhhhhhhhhhhhhhh...eeeeeee..hhhhhh.....eeee.....eeeee......hhhhhhhh........eeeeeeeeeehhhhhhhhhh..hhhhhhhh..hhhhhhh...eeeee.-----------....hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vh1 B   2 SFVVIIPARY------GKPLVDINGKPmIVHVLERARESGAERIIVATDHEDVARAVEAAGGEVCmTRA-----TERLAEVVEKCAFSDDTVIVNVQGDEPmIPATIIRQVADNLAQRQVGmATLAVPIHNAEEAFNPNAVKVVLDAEGYALYFSRATIPWDRDRFAEGLETVGDNFLRHLGIYGYRAGFIRRYVNWQPSPLEHIEmLEQLRVLWYGEKIHVAVA-----------EDLERVRAEm 247
                                    11      | 21       |31        41        51        61     |  |-    |   81        91       101 |     111       121 |     131       141       151       161       171       181       191       201      |211       221    |    -      |241     |
                                    11     18         29-MSE                                67-MSE   76                        103-MSE             123-MSE                                                                              208-MSE           226         238      247-MSE


Chain C from PDB  Type:PROTEIN  Length:233
 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 d1vh1c_ C: CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)synthetas    e                                                                                                                                                                               SCOP domains
               CATH domains 1vh1C00 C:2-246 Spore Coat Polysaccharide Biosynthesis Protein SpsA    ; Chain A                                                                                                                                                                     - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.........hhhh.ee..eehhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh..eeee.----..hhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhh...eeeeeee..hhhhhh.....eeee.....eeeee......hhhhhh-----.....eeeeeeeeeehhhhhhhhhh..hhhhhhhh..hhhhhhh...eeeee...----...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vh1 C   2 SFVVIIPARYASTRLPGKPLVDINGKPmIVHVLERARESGAERIIVATDHEDVARAVEAAGGEVCmT----QSGTERLAEVVEKCAFSDDTVIVNVQGDEPmIPATIIRQVADNLAQRQVGmATLAVPIHNAEEAFNPNAVKVVLDAEGYALYFSRATIPWDRDRFA-----VGDNFLRHLGIYGYRAGFIRRYVNWQPSPLEHIEmLEQLRVLWYGEKIHVAVAQE----GVDTPEDLERVRAEm 247
                                    11        21       |31        41        51        61     ||  - |      81        91       101 |     111       121 |     131       141       151       161      |  -  |    181       191       201      |211       221      |  - |     241     |
                                                      29-MSE                                67-MSE73                           103-MSE             123-MSE                                      168   174                               208-MSE             228  233           247-MSE
                                                                                             68                                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:241
 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 d1vh1d_ D: CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)synthetas     e                                                                                                                                                                              SCOP domains
               CATH domains 1vh1D00 D:2-246 Spore Coat Polysaccharide Biosynthesis Protein SpsA     ; Chain A                                                                                                                                                                    - CATH domains
           Pfam domains (1) --CTP_transf_3-1vh1D01 D:4-221                                                                                                                                                                                              -------------------------- Pfam domains (1)
           Pfam domains (2) --CTP_transf_3-1vh1D02 D:4-221                                                                                                                                                                                              -------------------------- Pfam domains (2)
           Pfam domains (3) --CTP_transf_3-1vh1D03 D:4-221                                                                                                                                                                                              -------------------------- Pfam domains (3)
           Pfam domains (4) --CTP_transf_3-1vh1D04 D:4-221                                                                                                                                                                                              -------------------------- Pfam domains (4)
         Sec.struct. author ..eeeee.........hhhh.ee..eehhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee.-----.hhhhhhhhhhhh......eeee........hhhhhhhhhhhhhh....eeeeeee..hhhhhh.....eeee.....eeeee......hhhhhhhh........eeeeeeeeeehhhhhhhh....hhhhhhhh..hhhhhhh...eeeee..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vh1 D   2 SFVVIIPARYASTRLPGKPLVDINGKPmIVHVLERARESGAERIIVATDHEDVARAVEAAGGEVCmT-----SGTERLAEVVEKCAFSDDTVIVNVQGDEPmIPATIIRQVADNLAQRQVGmATLAVPIHNAEEAFNPNAVKVVLDAEGYALYFSRATIPWDRDRFAEGLETVGDNFLRHLGIYGYRAGFIRRYVNWQPSPLEHIEmLEQLRVLWYGEKIHVAVAQEVPGTGVDTPEDLERVRAEm 247
                                    11        21       |31        41        51        61     ||  -  |     81        91       101 |     111       121 |     131       141       151       161       171       181       191       201      |211       221       231       241     |
                                                      29-MSE                                67-MSE 74                          103-MSE             123-MSE                                                                              208-MSE                                247-MSE
                                                                                             68
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological 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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 Related Entries

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

UniProtKB/Swiss-Prot
        KDSB_ECOLI | P04951: 3k8d 3k8e

(-) Related Entries Specified in the PDB File

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