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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 :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
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
    EC Number: 2.7.7.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: KDSB, HI0058
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: CMP-KDO SYNTHETASE, CMP-2-KETO-3-DEOXYOCTULOSONIC ACID SYNTHETASE, CKS

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1CMK2Ligand/IonCYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID
2MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1CMK1Ligand/IonCYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1CMK1Ligand/IonCYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1CMK-1Ligand/IonCYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID
2MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:8 , ALA A:9 , ARG A:10 , HIS A:72 , ASN A:73 , SER A:74 , ARG A:78 , GLN A:98 , GLY A:99 , ASP A:100 , VAL A:142 , ARG A:157 , LYS A:175 , HIS A:185 , TYR A:189 , GLU A:214 , GLN A:215 , HOH A:287 , HOH A:294 , HOH A:297 , HOH A:304BINDING SITE FOR RESIDUE CMK A 263
2AC2SOFTWAREARG A:164 , PRO B:8 , ALA B:9 , ARG B:10 , LYS B:19 , HIS B:72 , ASN B:73 , SER B:74 , GLY B:75 , ARG B:78 , GLN B:98 , GLY B:99 , ASP B:100 , ASN B:140 , VAL B:142 , ARG B:157 , HIS B:185 , TYR B:189 , LYS B:212 , LEU B:213 , GLU B:214 , GLN B:215 , VAL B:238 , HOH B:287BINDING SITE FOR RESIDUE CMK B 263

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VH3)

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VH3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VH3)

(-) Exons   (0, 0)

(no "Exon" information available for 1VH3)

(-) 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:211
 aligned with KDSB_HAEIN | P44490 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:228
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
           KDSB_HAEIN     2 SFTVIIPARFASSRLPGKPLADIKGKPMIQHVFEKALQSGASRVIIATDNENVADVAKSFGAEVCMTSVNHNSGTERLAEVVEKLAIPDNEIIVNIQGDEPLIPPVIVRQVADNLAKFNVNMASLAVKIHDAEELFNPNAVKVLTDKDGYVLYFSRSVIPYDRDQFMNLQDVQKVQLSDAYLRHIGIYAYRAGFIKQYVQWAPTQLENLEKLEQLRVLYNGERIHVEL 229
               SCOP domains d1vh3a_ A                 : CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)synthetase                                                                                                                                                SCOP domains
               CATH domains 1vh3A00 A                 :2-229 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.-----------------hhhhhhhhhhhhh....eeeee.hhhhhhhhhhh..eeee......hhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhh....eeeeee..hhhhhh.....eeee.....eeeee......hhhhhh..............eeeeeeeeeehhhhhhhhhh..hhhhhhhh..hhhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vh3 A   2 SFTVIIPAR-----------------PmIQHVFEKALQSGASRVIIATDNENVADVAKSFGAEVCmTSVNHNSGTERLAEVVEKLAIPDNEIIVNIQGDEPLIPPVIVRQVADNLAKFNVNmASLAVKIHDAEELFNPNAVKVLTDKDGYVLYFSRSVIPYDRDQFmNLQDVQKVQLSDAYLRHIGIYAYRAGFIKQYVQWAPTQLENLEKLEQLRVLYNGERIHVEL 229
                                    |-         -      ||31        41        51        61     |  71        81        91       101       111       121 |     131       141       151       161      |171       181       191       201       211       221        
                                   10                28|                                    67-MSE                                                 123-MSE                                      168-MSE                                                         
                                                      29-MSE                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:246
 aligned with KDSB_HAEIN | P44490 from UniProtKB/Swiss-Prot  Length:254

    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_HAEIN     2 SFTVIIPARFASSRLPGKPLADIKGKPMIQHVFEKALQSGASRVIIATDNENVADVAKSFGAEVCMTSVNHNSGTERLAEVVEKLAIPDNEIIVNIQGDEPLIPPVIVRQVADNLAKFNVNMASLAVKIHDAEELFNPNAVKVLTDKDGYVLYFSRSVIPYDRDQFMNLQDVQKVQLSDAYLRHIGIYAYRAGFIKQYVQWAPTQLENLEKLEQLRVLYNGERIHVELAKEVPAVGVDTAEDLEKVRA 249
               SCOP domains d1vh3b_ B:   CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)synthetase                                                                                                                                                                                   SCOP domains
               CATH domains 1vh3B00 B:2  -249 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...--.............hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh.eeee......hhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhh...eeeeeee..hhhhhh.....eeee.....eeeee......hhhhhh..............eeeeeeeeeehhhhhhhhhh..hhhhhhhh..hhhhhhh...eeeee..........hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vh3 B   2 SFTVIIPARFA--RLPGKPLADIKGKPmIQHVFEKALQSGASRVIIATDNENVADVAKSFGAEVCmTSVNHNSGTERLAEVVEKLAIPDNEIIVNIQGDEPLIPPVIVRQVADNLAKFNVNmASLAVKIHDAEELFNPNAVKVLTDKDGYVLYFSRSVIPYDRDQFmNLQDVQKVQLSDAYLRHIGIYAYRAGFIKQYVQWAPTQLENLEKLEQLRVLYNGERIHVELAKEVPAVGVDTAEDLEKVRA 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        
                                     12 15            29-MSE                                67-MSE                                                 123-MSE                                      168-MSE                                                                             


Chain C from PDB  Type:PROTEIN  Length:238
 aligned with KDSB_HAEIN | P44490 from UniProtKB/Swiss-Prot  Length:254

    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_HAEIN     2 SFTVIIPARFASSRLPGKPLADIKGKPMIQHVFEKALQSGASRVIIATDNENVADVAKSFGAEVCMTSVNHNSGTERLAEVVEKLAIPDNEIIVNIQGDEPLIPPVIVRQVADNLAKFNVNMASLAVKIHDAEELFNPNAVKVLTDKDGYVLYFSRSVIPYDRDQFMNLQDVQKVQLSDAYLRHIGIYAYRAGFIKQYVQWAPTQLENLEKLEQLRVLYNGERIHVELAKEVPAVGVDTAEDLEKVRA 249
               SCOP domains d1vh3c_ C: CMP:2-keto-3-deoxy-manno-octonic acid (CMP-KDO)synthetase                                                                                                                                                                                     SCOP domains
               CATH domains 1vh3C00 C:2-249 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                                             CATH domains
           Pfam domains (1) --CTP_transf_3-1vh3C01 C:4-225                                                                                                                                                                                                  ------------------------ Pfam domains (1)
           Pfam domains (2) --CTP_transf_3-1vh3C02 C:4-225                                                                                                                                                                                                  ------------------------ Pfam domains (2)
           Pfam domains (3) --CTP_transf_3-1vh3C03 C:4-225                                                                                                                                                                                                  ------------------------ Pfam domains (3)
         Sec.struct. author ..eeeee.........hhhh.ee..eehhhhhhhhhhhh...eeeeee.hhhhhhhhhhh..eeee......hhhhhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhh...eeeeeee..hhhhhh.....eeee.....eeeee...........----------.....eeeeeeeeeehhhhhhhhh...hhhhhhhh.hhhhhhhh....eeee..........hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vh3 C   2 SFTVIIPARFASSRLPGKPLADIKGKPmIQHVFEKALQSGASRVIIATDNENVADVAKSFGAEVCmTSVNHNSGTERLAEVVEKLAIPDNEIIVNIQGDEPLIPPVIVRQVADNLAKFNVNmASLAVKIHDAEELFNPNAVKVLTDKDGYVLYFSRSVIPYDRDQF----------LSDAYLRHIGIYAYRAGFIKQYVQWAPTQLENLEKLEQLRVLYNGERIHVELAKEVPAVGVDTAEDLEKVRA 249
                                    11        21       |31        41        51        61     |  71        81        91       101       111       121 |     131       141       151       161     |   -      |181       191       201       211       221       231       241        
                                                      29-MSE                                67-MSE                                                 123-MSE                                     167        178
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        KDSB_HAEIN | P44490: 1vic 3duv

(-) Related Entries Specified in the PDB File

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