Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE FROM YERSINIA PESTIS
 
Authors :  J. Osipiuk, M. Zhou, S. Grimshaw, W. F. Anderson, A. Joachimiak, Center Structural Genomics Of Infectious Diseases (Csgid)
Date :  12 Sep 09  (Deposition) - 22 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Idp02355, 3-Deoxy-Manno-Octulosonate Cytidylyltransferase, Lipopolysaccharide Biosynthesis, Nucleotidyltransferase, Transferase, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, M. Zhou, S. Grimshaw, W. F. Anderson, A. Joachimiak
X-Ray Crystal Structure Of 3-Deoxy-Manno-Octulosonate Cytidylyltransferase From Yersinia Pestis.
To Be Published
PubMed: search

(-) 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: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: KDSB, Y2772, YPO1400, YP_1193
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92
    Synonym: CMP-KDO SYNTHETASE, CMP-2-KETO-3-DEOXYOCTULOSONIC ACID SYNTHETASE, CKS

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1IMD2Ligand/IonIMIDAZOLE
2MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1IMD4Ligand/IonIMIDAZOLE
2MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:76 , MSE A:123 , TYR A:185 , TYR A:187 , TYR A:195 , GLN A:211BINDING SITE FOR RESIDUE IMD A 301
2AC2SOFTWAREPRO A:106 , VAL A:196 , HOH A:322BINDING SITE FOR RESIDUE IMD A 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile A:160 -Pro A:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3JTJ)

(-) 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:249
 aligned with KDSB_YERPE | Q8ZGA4 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:249
                                    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_YERPE     2 SFIAIIPARYASTRLPGKPLADIAGKPMVVHVMERALASGADRVIVATDHPDVVKAVEAAGGEVCLTRADHQSGTERLAEVIEHYGFADDDIIVNVQGDEPLVPPVIIRQVADNLAACSAGMATLAVPIASSEEAFNPNAVKVVMDAQGYALYFSRATIPWERERFAQSKETIGDCFLRHIGIYAYRAGFIRRYVNWAPSQLEQIELLEQLRVLWYGEKIHVAVAKAVPAVGVDTQSDLDRVRAIMLNQ 250
               SCOP domains d3jtja_ A: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains 3jtjA00 A:2-250 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                              CATH domains
               Pfam domains --CTP_transf_3-3jtjA01 A:4-221                                                                                                                                                                                              ----------------------------- Pfam domains
         Sec.struct. author ..eeeeee........hhhh.ee..eehhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee......hhhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhh...eeeeeee..hhhhhh.....eeee.....eeeee......hhhhhhhh........eeeeeeeeeehhhhhhhh....hhhhhhhh..hhhhhhh....eeee..........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3jtj A   2 SFIAIIPARYASTRLPGKPLADIAGKPmVVHVmERALASGADRVIVATDHPDVVKAVEAAGGEVCLTRADHQSGTERLAEVIEHYGFADDDIIVNVQGDEPLVPPVIIRQVADNLAACSAGmATLAVPIASSEEAFNPNAVKVVmDAQGYALYFSRATIPWERERFAQSKETIGDCFLRHIGIYAYRAGFIRRYVNWAPSQLEQIELLEQLRVLWYGEKIHVAVAKAVPAVGVDTQSDLDRVRAImLNQ 250
                                    11        21       |31  |     41        51        61        71        81        91       101       111       121 |     131       141    |  151       161       171       181       191       201       211       221       231       241     |   
                                                      29-MSE|                                                                                      123-MSE                146-MSE                                                                                              247-MSE
                                                           34-MSE
   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, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (KDSB_YERPE | Q8ZGA4)
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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    IMD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ile A:160 - Pro A:161   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3jtj
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  KDSB_YERPE | Q8ZGA4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.7.38
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  KDSB_YERPE | Q8ZGA4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3JTJ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3JTJ)