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(-) Description

Title :  P43 CRYSTAL OF DCTBP
 
Authors :  Y. F. Zhou, B. Y. Nan, X. Liu, J. Nan, Y. H. Liang, S. Panjikar, Q. J. Ma, Y. P D. Su
Date :  18 Oct 07  (Deposition) - 18 Nov 08  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Pas, Periplasmic Histidine Kinase, Inner Membrane, Membrane, Phosphorylation, Transferase, Transmembrane, Two-Component Regulatory System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. F. Zhou, B. Y. Nan, X. Liu, J. Nan, Y. H. Liang, S. Panjikar, Q. J. Ma, Y. P. Wang, X. -D. Su
Crystal Structures Of Sensory Histidine Kinase Dctbp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - C4-DICARBOXYLATE TRANSPORT SENSOR PROTEIN DCTB
    ChainsA, B, C, D
    EC Number2.7.13.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPERIPLASMIC SENSING DOMAIN
    GeneDCTB
    Organism CommonSINORHIZOBIUM MELILOTI
    Organism ScientificRHIZOBIUM MELILOTI

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MLA4Ligand/IonMALONIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MLA2Ligand/IonMALONIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MLA2Ligand/IonMALONIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:144 , TYR A:149 , ARG A:152 , TYR A:154 , GLY A:170 , THR A:171 , TYR A:179 , GLN A:252BINDING SITE FOR RESIDUE MLA A 1
2AC2SOFTWAREPHE B:144 , TYR B:149 , ARG B:152 , TYR B:154 , THR B:171 , TYR B:179 , GLN B:252 , HOH B:318BINDING SITE FOR RESIDUE MLA B 2
3AC3SOFTWARETYR C:124 , PHE C:144 , TYR C:149 , ARG C:152 , TYR C:154 , GLY C:170 , THR C:171 , TYR C:179 , GLN C:252BINDING SITE FOR RESIDUE MLA C 3
4AC4SOFTWAREPHE D:144 , TYR D:149 , ARG D:152 , TYR D:154 , GLY D:170 , THR D:171 , VAL D:172 , SER D:173 , TYR D:179 , GLN D:252BINDING SITE FOR RESIDUE MLA D 4

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp C:283 -Ser C:284

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZBB)

(-) 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:255
 aligned with DCTB_RHIME | P13633 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:255
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     
           DCTB_RHIME    54 LAGLAGQSRIDASLKASLLRAVVERQRALPLVLADDAAIRGALLSPDRPSLDRINRKLEALATSAEAAVIYLIDRSGVAVAASNWQEPTSFVGNDYAFRDYFRLAVRDGMAEHFAMGTVSNRPGLYISRRVDGPGGPLGVIVAKLEFDGVEADWQASGKPAYVTDRRGIVLITSLPSWRFMTTKPIAEDRLAPIRESLQFGDAPLLPLPFRKIEARPDGSSTLDALLPGDSTAAFLRVETMVPSTNWRLEQLSPL 308
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeee....eeee...................hhhhhhhheeeeeee......eeeeeeeeeee..eeeeeeeeee.hhhhhhhhhhhh..eeee.....eeee.hhhhh.......hhhhhhhhhhhh............eeeee.....eeeee.......eeeeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zbb A  54 LAGLAGQSRIDASLKASLLRAVVERQRALPLVLADDAAIRGALLSPDRPSLDRINRKLEALATSAEAAVIYLIDRSGVAVAASNWQEPTSFVGNDYAFRDYFRLAVRDGMAEHFAMGTVSNRPGLYISRRVDGPGGPLGVIVAKLEFDGVEADWQASGKPAYVTDRRGIVLITSLPSWRFMTTKPIAEDRLAPIRESLQFGDAPLLPLPFRKIEARPDGSSTLDALLPGDSTAAFLRVETMVPSTNWRLEQLSPL 308
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with DCTB_RHIME | P13633 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:255
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     
           DCTB_RHIME    54 LAGLAGQSRIDASLKASLLRAVVERQRALPLVLADDAAIRGALLSPDRPSLDRINRKLEALATSAEAAVIYLIDRSGVAVAASNWQEPTSFVGNDYAFRDYFRLAVRDGMAEHFAMGTVSNRPGLYISRRVDGPGGPLGVIVAKLEFDGVEADWQASGKPAYVTDRRGIVLITSLPSWRFMTTKPIAEDRLAPIRESLQFGDAPLLPLPFRKIEARPDGSSTLDALLPGDSTAAFLRVETMVPSTNWRLEQLSPL 308
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeeee....eeee................hhhhhhhhhhheeeeeee......eeeeeeeeee....eeeeeeeee.hhhhhhhhhh....eeee.....eeee.hhhhh.......hhhhhhhhhhhhh............eeeee...eeeee.........eeeeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zbb B  54 LAGLAGQSRIDASLKASLLRAVVERQRALPLVLADDAAIRGALLSPDRPSLDRINRKLEALATSAEAAVIYLIDRSGVAVAASNWQEPTSFVGNDYAFRDYFRLAVRDGMAEHFAMGTVSNRPGLYISRRVDGPGGPLGVIVAKLEFDGVEADWQASGKPAYVTDRRGIVLITSLPSWRFMTTKPIAEDRLAPIRESLQFGDAPLLPLPFRKIEARPDGSSTLDALLPGDSTAAFLRVETMVPSTNWRLEQLSPL 308
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     

Chain C from PDB  Type:PROTEIN  Length:255
 aligned with DCTB_RHIME | P13633 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:255
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     
           DCTB_RHIME    54 LAGLAGQSRIDASLKASLLRAVVERQRALPLVLADDAAIRGALLSPDRPSLDRINRKLEALATSAEAAVIYLIDRSGVAVAASNWQEPTSFVGNDYAFRDYFRLAVRDGMAEHFAMGTVSNRPGLYISRRVDGPGGPLGVIVAKLEFDGVEADWQASGKPAYVTDRRGIVLITSLPSWRFMTTKPIAEDRLAPIRESLQFGDAPLLPLPFRKIEARPDGSSTLDALLPGDSTAAFLRVETMVPSTNWRLEQLSPL 308
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...eeeeee....eeee................hhhhhhhhhhheeeeeee......eeeeeeeeeee..eeeeeeeeee.hhhhhhhhhh....eeee.....eeee.hhhhh.......hhhhhhhhhhhh......................eeeee.......eeeeeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zbb C  54 LAGLAGQSRIDASLKASLLRAVVERQRALPLVLADDAAIRGALLSPDRPSLDRINRKLEALATSAEAAVIYLIDRSGVAVAASNWQEPTSFVGNDYAFRDYFRLAVRDGMAEHFAMGTVSNRPGLYISRRVDGPGGPLGVIVAKLEFDGVEADWQASGKPAYVTDRRGIVLITSLPSWRFMTTKPIAEDRLAPIRESLQFGDAPLLPLPFRKIEARPDGSSTLDALLPGDSTAAFLRVETMVPSTNWRLEQLSPL 308
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     

Chain D from PDB  Type:PROTEIN  Length:255
 aligned with DCTB_RHIME | P13633 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:255
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     
           DCTB_RHIME    54 LAGLAGQSRIDASLKASLLRAVVERQRALPLVLADDAAIRGALLSPDRPSLDRINRKLEALATSAEAAVIYLIDRSGVAVAASNWQEPTSFVGNDYAFRDYFRLAVRDGMAEHFAMGTVSNRPGLYISRRVDGPGGPLGVIVAKLEFDGVEADWQASGKPAYVTDRRGIVLITSLPSWRFMTTKPIAEDRLAPIRESLQFGDAPLLPLPFRKIEARPDGSSTLDALLPGDSTAAFLRVETMVPSTNWRLEQLSPL 308
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeeee....eeee................hhhhhhhhhhheeeeeee......eeeeeeeeeee..eeeeeeeeee.hhhhhhhhhh....eeee.....eeee.hhhhh.......hhhhhhhhhhhhh..........ee..........eeee.......eeeeeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zbb D  54 LAGLAGQSRIDASLKASLLRAVVERQRALPLVLADDAAIRGALLSPDRPSLDRINRKLEALATSAEAAVIYLIDRSGVAVAASNWQEPTSFVGNDYAFRDYFRLAVRDGMAEHFAMGTVSNRPGLYISRRVDGPGGPLGVIVAKLEFDGVEADWQASGKPAYVTDRRGIVLITSLPSWRFMTTKPIAEDRLAPIRESLQFGDAPLLPLPFRKIEARPDGSSTLDALLPGDSTAAFLRVETMVPSTNWRLEQLSPL 308
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     

   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 2ZBB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DCTB_RHIME | P13633)
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:0004673    protein histidine kinase activity    Catalysis of the reaction: ATP + protein L-histidine = ADP + protein phospho-L-histidine.
    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:0018106    peptidyl-histidine phosphorylation    The phosphorylation of peptidyl-histidine to form peptidyl-1'-phospho-L-histidine (otherwise known as tau-phosphohistidine, tele-phosphohistidine) or peptidyl-3'-phospho-L-histidine (otherwise known as pi-phosphohistidine, pros-phosphohistidine).
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DCTB_RHIME | P136333e4o 3e4p 3e4q 4gkg

(-) Related Entries Specified in the PDB File

2qhh SUCCINATE BOUND
2qhi P21 SPACEGROUP, MALONATE BOUND
2qhj P21 SPACE GROUP, APO