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(-) Description

Title :  EVIDENCE FOR A TWO-METAL-ION-MECHANISM IN THE KDO-CYTIDYLYLTRANSFERASE KDSB
 
Authors :  H. Schmidt, J. R. Mesters, U. Mamat, R. Hilgenfeld
Date :  25 Jan 11  (Deposition) - 24 Aug 11  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Transferase, Lipid A (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Schmidt, J. R. Mesters, J. Wu, R. W. Woodard, R. Hilgenfeld, U. Mamat
Evidence For A Two-Metal-Ion Mechanism In The Cytidyltransferase Kdsb, An Enzyme Involved In Lipopolysaccharide Biosynthesis.
Plos One V. 6 23231 2011
PubMed-ID: 21826242  |  Reference-DOI: 10.1371/JOURNAL.PONE.0023231

(-) 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 Plasmid: PT7-KDSB
    Expression System Strain: BL21 CODONPLUS(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PRIL
    Expression System Vector Type: PLASMID
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: CYTIDYLTRANSFERASE, CMP-2-KETO-3-DEOXYOCTULOSONIC ACID SYNTHASE, CKS, CMP-KDO SYNTHASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CTP3Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
3IPA2Ligand/IonISOPROPYL ALCOHOL
4MG6Ligand/IonMAGNESIUM ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CTP2Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
3IPA1Ligand/IonISOPROPYL ALCOHOL
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1BME-1Ligand/IonBETA-MERCAPTOETHANOL
2CTP2Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
3IPA2Ligand/IonISOPROPYL ALCOHOL
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:8 , ALA A:9 , ARG A:10 , SER A:13 , THR A:14 , ARG A:15 , LYS A:19 , LEU A:70 , PRO A:71 , SER A:72 , GLY A:73 , ARG A:76 , GLY A:94 , ASP A:95 , ASP A:219 , MG A:1234 , MG A:1235 , HOH A:2014 , HOH A:2056 , HOH A:2058 , HOH A:2059 , HOH A:2060 , HOH A:2061 , LYS B:232 , ASN B:233 , HOH B:2104BINDING SITE FOR RESIDUE CTP A1233
02AC2SOFTWAREPRO B:8 , ALA B:9 , ARG B:10 , SER B:13 , THR B:14 , ARG B:15 , LYS B:19 , LEU B:70 , PRO B:71 , SER B:72 , GLY B:73 , ARG B:76 , GLN B:93 , GLY B:94 , ASP B:95 , ASP B:219 , MG B:1236 , MG B:1237 , HOH B:2031 , HOH B:2106 , HOH B:2107 , HOH B:2108 , HOH B:2109 , HOH B:2110 , HOH B:2111 , HOH B:2112BINDING SITE FOR RESIDUE CTP B1235
03AC3SOFTWAREPRO C:8 , ALA C:9 , ARG C:10 , SER C:13 , THR C:14 , ARG C:15 , LYS C:19 , LEU C:70 , PRO C:71 , SER C:72 , GLY C:73 , ARG C:76 , GLN C:93 , GLY C:94 , ASP C:95 , ASP C:219 , MG C:1233 , MG C:1234 , HOH C:2016 , HOH C:2017 , HOH C:2018 , HOH C:2019BINDING SITE FOR RESIDUE CTP C1232
04AC4SOFTWARELYS A:19 , ASP A:95 , ASP A:219 , CTP A:1233 , HOH A:2014 , HOH A:2015 , HOH A:2056BINDING SITE FOR RESIDUE MG A1234
05AC5SOFTWARELYS B:19 , ASP B:95 , ASP B:219 , CTP B:1235 , HOH B:2031 , HOH B:2095 , HOH B:2108BINDING SITE FOR RESIDUE MG B1236
06AC6SOFTWAREASP C:95 , ASP C:219 , CTP C:1232 , HOH C:2015BINDING SITE FOR RESIDUE MG C1233
07AC7SOFTWARECTP A:1233 , HOH A:2061 , ASN B:233 , HOH B:2104BINDING SITE FOR RESIDUE MG A1235
08AC8SOFTWARECTP B:1235 , HOH B:2109 , HOH B:2110 , HOH B:2111BINDING SITE FOR RESIDUE MG B1237
09AC9SOFTWARECTP C:1232 , HOH C:2016 , HOH C:2017 , HOH C:2018BINDING SITE FOR RESIDUE MG C1234
10BC1SOFTWARESER C:74 , ASN C:91 , PHE C:180 , GLU C:195BINDING SITE FOR RESIDUE IPA C1235
11BC2SOFTWAREGLU A:195BINDING SITE FOR RESIDUE IPA A1236
12BC3SOFTWAREGLU A:126 , GLU A:129 , ARG B:2 , ASP B:87 , GLU B:112 , HOH B:2044BINDING SITE FOR RESIDUE BME A1237

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y6P)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ile A:152 -Pro A:153
2Tyr A:162 -Pro A:163
3Ile B:152 -Pro B:153
4Tyr B:162 -Pro B:163
5Ile C:152 -Pro C:153
6Tyr C:162 -Pro C:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y6P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y6P)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y6P)

(-) 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:231
 aligned with KDSB_AQUAE | O66914 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 
           KDSB_AQUAE     2 RRAVIIPARLGSTRLKEKPLKNLLGKPLIRWVVEGLVKTGERVILATDSERVKEVVEDLCEVFLTPSDLPSGSDRVLYVVRDLDVDLIINYQGDEPFVYEEDIKLIFRELEKGERVVTLARKDKEAYERPEDVKVVLDREGYALYFSRSPIPYFRKNDTFYPLKHVGIYGFRKETLMEFGAMPPSKLEQIEGLEQLRLLENGIKIKVLITENYYHGVDTEEDLKIVEEKLK 232
               SCOP domains d2y6pa_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........hhhh.ee..eehhhhhhhhhhh....eeeee.hhhhhhhhh...eeee......hhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhh..eeeeeee.hhhhhh....eeee.....eeeee...............eeeeeeeeeehhhhhhhhhh..hhhhhhhh.hhhhhhhh....eeee.........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y6p A   2 RRAVIIPARLGSTRLKEKPLKNLLGKPLIRWVVEGLVKTGERVILATDSERVKEVVEDLCEVFLTPSDLPSGSDRVLYVVRDLDVDLIINYQGDEPFVYEEDIKLIFRELEKGERVVTLARKDKEAYERPEDVKVVLDREGYALYFSRSPIPYFRKNDTFYPLKHVGIYGFRKETLMEFGAMPPSKLEQIEGLEQLRLLENGIKIKVLITENYYHGVDTEEDLKIVEEKLK 232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 


Chain B from PDB  Type:PROTEIN  Length:233
 aligned with KDSB_AQUAE | O66914 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:233
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231   
           KDSB_AQUAE     2 RRAVIIPARLGSTRLKEKPLKNLLGKPLIRWVVEGLVKTGERVILATDSERVKEVVEDLCEVFLTPSDLPSGSDRVLYVVRDLDVDLIINYQGDEPFVYEEDIKLIFRELEKGERVVTLARKDKEAYERPEDVKVVLDREGYALYFSRSPIPYFRKNDTFYPLKHVGIYGFRKETLMEFGAMPPSKLEQIEGLEQLRLLENGIKIKVLITENYYHGVDTEEDLKIVEEKLKNL 234
               SCOP domains d2y6pb_ B: automated matches                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........hhhh.ee..eehhhhhhhhhhh....eeeee.hhhhhhhhh...eeee......hhhhhhhhhhh.....eeee........hhhhhhhhhhhhhh...eeeeeee...........eeee.....eeeee...............eeeeeeeeeehhhhhhhhhh..hhhhhhhh.hhhhhhhh....eeee.........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y6p B   2 RRAVIIPARLGSTRLKEKPLKNLLGKPLIRWVVEGLVKTGERVILATDSERVKEVVEDLCEVFLTPSDLPSGSDRVLYVVRDLDVDLIINYQGDEPFVYEEDIKLIFRELEKGERVVTLARKDKEAYERPEDVKVVLDREGYALYFSRSPIPYFRKNDTFYPLKHVGIYGFRKETLMEFGAMPPSKLEQIEGLEQLRLLENGIKIKVLITENYYHGVDTEEDLKIVEEKLKNL 234
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231   


Chain C from PDB  Type:PROTEIN  Length:229
 aligned with KDSB_AQUAE | O66914 from UniProtKB/Swiss-Prot  Length:234

    Alignment length:229
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222         
           KDSB_AQUAE     3 RAVIIPARLGSTRLKEKPLKNLLGKPLIRWVVEGLVKTGERVILATDSERVKEVVEDLCEVFLTPSDLPSGSDRVLYVVRDLDVDLIINYQGDEPFVYEEDIKLIFRELEKGERVVTLARKDKEAYERPEDVKVVLDREGYALYFSRSPIPYFRKNDTFYPLKHVGIYGFRKETLMEFGAMPPSKLEQIEGLEQLRLLENGIKIKVLITENYYHGVDTEEDLKIVEEKL 231
               SCOP domains d2y6pc_ C: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.........hhhh.ee..eehhhhhhhhhhh....eeeee.hhhhhhhhh...eeee......hhhhhhhhhhh.....eeee........hhhhhhhhhhhhhhh..eeeeeee...........eeee.....eeeee...............eeeeeeeeeehhhhhhhhh...hhhhhhhh.hhhhhhhh...eeeee.........hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y6p C   3 RAVIIPARLGSTRLKEKPLKNLLGKPLIRWVVEGLVKTGERVILATDSERVKEVVEDLCEVFLTPSDLPSGSDRVLYVVRDLDVDLIINYQGDEPFVYEEDIKLIFRELEKGERVVTLARKDKEAYERPEDVKVVLDREGYALYFSRSPIPYFRKNDTFYPLKHVGIYGFRKETLMEFGAMPPSKLEQIEGLEQLRLLENGIKIKVLITENYYHGVDTEEDLKIVEEKL 231
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
   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  (0, 0)

(no "CATH Domain" information available for 2Y6P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y6P)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (KDSB_AQUAE | O66914)
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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