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(-) Description

Title :  STRUCTURE OF THE 3-DEOXY-D-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE (KDSB) FROM COXIELLA BURNETII
 
Authors :  M. C. Franklin, J. Cheung, M. Rudolph, M. Cassidy, E. Gary, F. Burshteyn
Date :  09 Sep 11  (Deposition) - 26 Oct 11  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Cell Envelope, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Franklin, J. Cheung, M. J. Rudolph, F. Burshteyn, M. Cassidy, E. Gary, B. Hillerich, Z. K. Yao, P. R. Carlier, M. Totrov, J. D. Love
Structural Genomics For Drug Design Against The Pathogen Coxiella Burnetii.
Proteins V. 83 2124 2015
PubMed-ID: 26033498  |  Reference-DOI: 10.1002/PROT.24841

(-) Compounds

Molecule 1 - 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
    Chains: A
    EC Number: 2.7.7.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CBU_0479, KDSB
    Organism Scientific: COXIELLA BURNETII
    Organism Taxid: 777
    Strain: RSA 493 NINE MILE PHASE I
    Synonym: CMP-2-KETO-3-DEOXYOCTULOSONIC ACID SYNTHASE, CKS, CMP-KDO SYNTHASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MSE4Mod. Amino AcidSELENOMETHIONINE
3NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
3NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:173 , GLN A:175 , HOH A:294 , HOH A:297BINDING SITE FOR RESIDUE NI A 300
2AC2SOFTWAREGLN A:31 , TYR A:34 , GLU A:35 , PHE A:61 , HOH A:393BINDING SITE FOR RESIDUE ACT A 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile A:161 -Pro A:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 3TQD)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:243
 aligned with KDSB_COXBU | Q83E52 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:248
                                    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_COXBU     2 EFRVIIPARFDSTRLPGKALVDIAGKPMIQHVYESAIKSGAEEVVIATDDKRIRQVAEDFGAVVCMTSSDHQSGTERIAEAAVALGFEDDEIIVCLQGDEPLIPPDAIRKLAEDLDEHDNVKVASLCTPITEVDELFNPHSTKVVLNRRNYALYFSHAPIPWGRDTFSDKENLQLNGSHYRHVGIYAYRVGFLEEYLSWDACPAEKMEALEQLRILWHGGRIHMVVAKSKCPPGVDTEEDLERVRAYF 249
               SCOP domains d3tqda_ A:    automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....---..hhhh.ee..eehhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee......hhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhh.--.eeeeeee..hhhhhh.....eeee.....eeeee............hhhhh......eeeeeeeeeehhhhhhhhhh..hhhhhhhh..hhhhhhh....eeee..........hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tqd A   2 EFRVIIPARFD---LPGKALVDIAGKPmIQHVYESAIKSGAEEVVIATDDKRIRQVAEDFGAVVCmTSSDHQSGTERIAEAAVALGFEDDEIIVCLQGDEPLIPPDAIRKLAEDLDEHD--KVASLCTPITEVDELFNPHSTKVVLNRRNYALYFSHAPIPWGRDTFSDKENLQLNGSHYRHVGIYAYRVGFLEEYLSWDACPAEKmEALEQLRILWHGGRIHmVVAKSKCPPGVDTEEDLERVRAYF 249
                                    11|   |   21       |31        41        51        61     |  71        81        91       101       111        |- |     131       141       151       161       171       181       191       201      |211       221   |   231       241        
                                     12  16           29-MSE                                67-MSE                                              120  |                                                                                  208-MSE          225-MSE                    
                                                                                                                                                   123
   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TQD)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (KDSB_COXBU | Q83E52)
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.
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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