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(-) Description

Title :  CRYSTAL STRUCTURE OF THE V. CHOLERAE HISTIDINE KINASE DCTB SENSOR DOMAIN
 
Authors :  J. Cheung, W. A. Hendrickson
Date :  15 Jan 08  (Deposition) - 12 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Histidine Kinase Sensor Domain, Phosphoprotein, Transferase, Two-Component Regulatory System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Cheung, W. A. Hendrickson
Crystal Structures Of C4-Dicarboxylate Ligand Complexes With Sensor Domains Of Histidine Kinases Dcus And Dctb.
J. Biol. Chem. V. 283 30256 2008
PubMed-ID: 18701447  |  Reference-DOI: 10.1074/JBC.M805253200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SENSOR PROTEIN
    ChainsA, B
    EC Number2.7.13.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B+
    Expression System StrainBL21(DE3)
    Expression System Vector TypePLASMID
    FragmentRESIDUES 28-286
    GeneVC1925
    Organism ScientificVIBRIO CHOLERAE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
3SIN2Ligand/IonSUCCINIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
3SIN1Ligand/IonSUCCINIC ACID
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
3SIN1Ligand/IonSUCCINIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:62 , ASP A:66 , HOH A:427 , HOH A:428 , LEU B:62 , ASP B:66BINDING SITE FOR RESIDUE CA A 1
2AC2SOFTWAREASP A:263 , LYS A:284 , HOH A:337 , HOH A:425 , HOH A:435 , HOH A:436BINDING SITE FOR RESIDUE CA A 2
3AC3SOFTWARETYR A:102 , PHE A:122 , PHE A:127 , ARG A:130 , TYR A:132 , GLY A:148 , SER A:149 , THR A:150 , SER A:151 , TYR A:157 , LYS A:175BINDING SITE FOR RESIDUE SIN A 287
4AC4SOFTWARETYR B:102 , PHE B:122 , PHE B:127 , ARG B:130 , TYR B:132 , GLY B:148 , SER B:149 , THR B:150 , SER B:151 , TYR B:157 , LYS B:175BINDING SITE FOR RESIDUE SIN B 288

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BY9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BY9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BY9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BY9)

(-) Exons   (0, 0)

(no "Exon" information available for 3BY9)

(-) 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:259
 aligned with Q9KQS3_VIBCH | Q9KQS3 from UniProtKB/TrEMBL  Length:597

    Alignment length:259
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276         
         Q9KQS3_VIBCH    27 WRFQYQALLNEHQSQLDRFSSHIVATLDKYAHIPHLISKDKELVDALLSAQNSAQIDITNRYLEQVNEVIQAADTYLIDRFGNTIASSNWNLDRSFIGRNFAWRPYFYLSIAGQKSQYFALGSTSGQRGYYYAYPVIYAAEILGVIVVKMDLSAIEQGWQNKSSYFVATDDHQVVFMSSQPAWLFHSVADLSPAQLNDIRQSQQYLDSPIPSLGWQGDLQAEQSEWRKPEKHWLQDDYIVSSRPLPELALTIRVLSPKI 285
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..eeeeee....eeee................hhhhhhhh....eeeeee......eeeeeeeeeee..eeeeeeeeee.hhhhhhh......eeeee.....eeee.hhhhh.......hhhhhhhhhhhh...................eeee...........eeeeeeeehhhheeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3by9 A  27 mRFQYQALLNEHQSQLDRFSSHIVATLDKYAHIPHLISKDKELVDALLSAQNSAQIDITNRYLEQVNEVIQAADTYLIDRFGNTIASSNWNLDRSFIGRNFAWRPYFYLSIAGQKSQYFALGSTSGQRGYYYAYPVIYAAEILGVIVVKmDLSAIEQGWQNKSSYFVATDDHQVVFmSSQPAWLFHSVADLSPAQLNDIRQSQQYLDSPIPSLGWQGDLQAEQSEWRKPEKHWLQDDYIVSSRPLPELALTIRVLSPKI 285
                            |       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196      |206       216       226       236       246       256       266       276         
                            |                                                                                                                                                  176-MSE                    203-MSE                                                                              
                           27-MSE                                                                                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:258
 aligned with Q9KQS3_VIBCH | Q9KQS3 from UniProtKB/TrEMBL  Length:597

    Alignment length:258
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278        
         Q9KQS3_VIBCH    29 FQYQALLNEHQSQLDRFSSHIVATLDKYAHIPHLISKDKELVDALLSAQNSAQIDITNRYLEQVNEVIQAADTYLIDRFGNTIASSNWNLDRSFIGRNFAWRPYFYLSIAGQKSQYFALGSTSGQRGYYYAYPVIYAAEILGVIVVKMDLSAIEQGWQNKSSYFVATDDHQVVFMSSQPAWLFHSVADLSPAQLNDIRQSQQYLDSPIPSLGWQGDLQAEQSEWRKPEKHWLQDDYIVSSRPLPELALTIRVLSPKIE 286
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..eeeeee....eeee................hhhhhhhh....eeeeee......eeeeeeeeeee..eeeeeeeeee.hhhhhh.......eeeee.....eeee.hhhhh.......hhhhhhhhhhhh...................eeee...........eeeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3by9 B  29 FQYQALLNEHQSQLDRFSSHIVATLDKYAHIPHLISKDKELVDALLSAQNSAQIDITNRYLEQVNEVIQAADTYLIDRFGNTIASSNWNLDRSFIGRNFAWRPYFYLSIAGQKSQYFALGSTSGQRGYYYAYPVIYAAEILGVIVVKmDLSAIEQGWQNKSSYFVATDDHQVVFmSSQPAWLFHSVADLSPAQLNDIRQSQQYLDSPIPSLGWQGDLQAEQSEWRKPEKHWLQDDYIVSSRPLPELALTIRVLSPKIE 286
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198    |  208       218       228       238       248       258       268       278        
                                                                                                                                                                             176-MSE                    203-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  (0, 0)

(no "SCOP Domain" information available for 3BY9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3BY9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BY9)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9KQS3_VIBCH | Q9KQS3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0000155    phosphorelay sensor kinase activity    Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
    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.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    GO:0015740    C4-dicarboxylate transport    The directed movement of a C4-dicarboxylate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A C4-dicarboxylate is the anion of a dicarboxylic acid that contains four carbon atoms.
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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3by8 CRYSTAL STRUCTURE OF THE E.COLI DCUS SENSOR DOMAIN