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(-) Description

Title :  CRYSTAL STRUCTURE OF 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE FROM HAEMOPHILUS INFLUENZAE COMPLEXED WITH THE SUBSTRATE 3-DEOXY-MANNO-OCTULOSONATE IN THE-CONFIGURATION
 
Authors :  H. J. Yoon, M. J. Ku, B. Mikami, S. W. Suh
Date :  18 Jul 08  (Deposition) - 09 Dec 08  (Release) - 09 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cmp-Kdo Synthetase, 3-Deoxy-Manno-Octulosonate Cytidylyltransferase, 3-Deoxy-Manno-Octulosonate, Kdsb, Cytoplasm, Lipopolysaccharide Biosynthesis, Nucleotidyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Yoon, M. J. Ku, B. Mikami, S. W. Suh
Structure Of 3-Deoxy-Manno-Octulosonate Cytidylyltransferase From Haemophilus Influenzae Complexed With The Substrate 3-Deoxy-Manno-Octulosonate In The Beta-Configuration.
Acta Crystallogr. , Sect. D V. 64 1292 2008
PubMed-ID: 19018107  |  Reference-DOI: 10.1107/S0907444908036342
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE
    Chains: A, B
    EC Number: 2.7.7.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: KDSB
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: CMP-KDO SYNTHETASE, CMP-2-KETO-3-DEOXYOCTULOSONIC ACID SYNTHETASE, CKS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1KDO2Ligand/Ion3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
2MSE10Mod. Amino AcidSELENOMETHIONINE
3P4C1Ligand/IonO-ACETALDEHYDYL-HEXAETHYLENE GLYCOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:98 , ARG A:157 , LYS A:175 , HIS A:185 , GLY A:187 , TYR A:189 , LEU A:213 , GLU A:214 , GLN A:215 , HOH A:309 , HOH A:310 , HOH A:411BINDING SITE FOR RESIDUE KDO A 263
2AC2SOFTWAREGLN B:98 , ASP B:100 , ARG B:157 , HIS B:185 , GLY B:187 , TYR B:189 , LYS B:212 , GLU B:214 , GLN B:215 , ASP B:239 , HOH B:341 , HOH B:501 , HOH B:799BINDING SITE FOR RESIDUE KDO B 263
3AC3SOFTWAREASN A:73 , PRO A:204 , GLN A:206 , ASN A:209 , LYS A:212 , HOH A:322 , HOH A:493 , HIS B:72 , GLU B:81BINDING SITE FOR RESIDUE P4C A 270

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ile A:160 -Pro A:161
2Ile B:160 -Pro B:161
3Val B:233 -Pro B:234

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DUV)

(-) 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:238
 aligned with KDSB_HAEIN | P44490 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:254
                                    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_HAEIN     1 MSFTVIIPARFASSRLPGKPLADIKGKPMIQHVFEKALQSGASRVIIATDNENVADVAKSFGAEVCMTSVNHNSGTERLAEVVEKLAIPDNEIIVNIQGDEPLIPPVIVRQVADNLAKFNVNMASLAVKIHDAEELFNPNAVKVLTDKDGYVLYFSRSVIPYDRDQFMNLQDVQKVQLSDAYLRHIGIYAYRAGFIKQYVQWAPTQLENLEKLEQLRVLYNGERIHVELAKEVPAVGVDTAEDLEKVRAILAAN 254
               SCOP domains d3duva_ A:                 automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains -3duvA00 A                :2-254 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..----------------.hhhhhhhhhhhh....eeeeee.hhhhhhhhh....eeee......hhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhh...eeeeeee..hhhhhh.....eeee.....eeeee......hhhhhh...hhhhh......eeeeeeeeeehhhhhhhh....hhhhhhhh..hhhhhhh...eeeeee.........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3duv A   1 mSFTVIIPAR----------------KPmIQHVFEKALQSGASRVIIATDNENVADVAKSFGAEVCmTSVNHNSGTERLAEVVEKLAIPDNEIIVNIQGDEPLIPPVIVRQVADNLAKFNVNmASLAVKIHDAEELFNPNAVKVLTDKDGYVLYFSRSVIPYDRDQFmNLQDVQKVQLSDAYLRHIGIYAYRAGFIKQYVQWAPTQLENLEKLEQLRVLYNGERIHVELAKEVPAVGVDTAEDLEKVRAILAAN 254
                            |       10         -      | 30        40        50        60      | 70        80        90       100       110       120  |    130       140       150       160       170       180       190       200       210       220       230       240       250    
                            |       10               27 |                                    67-MSE                                                 123-MSE                                      168-MSE                                                                                  
                            1-MSE                      29-MSE                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:254
 aligned with KDSB_HAEIN | P44490 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:254
                                    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_HAEIN     1 MSFTVIIPARFASSRLPGKPLADIKGKPMIQHVFEKALQSGASRVIIATDNENVADVAKSFGAEVCMTSVNHNSGTERLAEVVEKLAIPDNEIIVNIQGDEPLIPPVIVRQVADNLAKFNVNMASLAVKIHDAEELFNPNAVKVLTDKDGYVLYFSRSVIPYDRDQFMNLQDVQKVQLSDAYLRHIGIYAYRAGFIKQYVQWAPTQLENLEKLEQLRVLYNGERIHVELAKEVPAVGVDTAEDLEKVRAILAAN 254
               SCOP domains d3duvb_ B: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -3duvB00 B:2-254 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee........hhhh.ee..eehhhhhhhhhhh....eeeeee.hhhhhhhhhhh..eeee......hhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhh....eeee.....eeeee......hhhhhh...hhhhh......eeeeeeeeeehhhhhhhhhh..hhhhhhhh..hhhhhhh...eeeee..........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3duv B   1 mSFTVIIPARFASSRLPGKPLADIKGKPmIQHVFEKALQSGASRVIIATDNENVADVAKSFGAEVCmTSVNHNSGTERLAEVVEKLAIPDNEIIVNIQGDEPLIPPVIVRQVADNLAKFNVNmASLAVKIHDAEELFNPNAVKVLTDKDGYVLYFSRSVIPYDRDQFmNLQDVQKVQLSDAYLRHIGIYAYRAGFIKQYVQWAPTQLENLEKLEQLRVLYNGERIHVELAKEVPAVGVDTAEDLEKVRAILAAN 254
                            |       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    
                            1-MSE                      29-MSE                                67-MSE                                                 123-MSE                                      168-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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KDSB_HAEIN | P44490)
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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        KDSB_HAEIN | P44490: 1vh3 1vic

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