Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE MG+2/BEF3-BOUND RECEIVER DOMAIN OF KDP POTASSIUM TRANSPORT SYSTEM RESPONSE REGULATOR KDPE
 
Authors :  A. Toro-Roman, T. Wu, A. M. Stock
Date :  22 Apr 05  (Deposition) - 13 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Two-Component System, Gene Regulation, Transcription Factor, Kdp Potassium Transport System, Doubly Wound Five-Stranded Beta-Alpha Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Toro-Roman, T. Wu, A. M. Stock
A Common Dimerization Interface In Bacterial Response Regulators Kdpe And Torr.
Protein Sci. V. 14 3077 2005
PubMed-ID: 16322582  |  Reference-DOI: 10.1110/PS.051722805
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KDP OPERON TRANSCRIPTIONAL REGULATORY PROTEIN KDPE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PEF27 (PJES307 DERIVATIVE)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL RECEIVER DOMAIN (RESIDUES 1-121)
    Gene: KDPE
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1BEF2Ligand/IonBERYLLIUM TRIFLUORIDE ION
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:9 , ASP A:52 , GLY A:54 , BEF A:301 , HOH A:352BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWAREASP B:9 , ASP B:52 , GLY B:54 , BEF B:302 , HOH B:357 , HOH B:358BINDING SITE FOR RESIDUE MG B 202
3AC3SOFTWAREASP A:52 , LEU A:53 , GLY A:54 , SER A:79 , ALA A:80 , LYS A:101 , MG A:201 , HOH A:352BINDING SITE FOR RESIDUE BEF A 301
4AC4SOFTWAREASP B:52 , LEU B:53 , GLY B:54 , SER B:79 , ALA B:80 , LYS B:101 , MG B:202 , HOH B:357BINDING SITE FOR RESIDUE BEF B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZH4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:101 -Pro A:102
2Lys B:101 -Pro B:102

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZH4)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RESPONSE_REGULATORYPS50110 Response regulatory domain profile.KDPE_ECOLI3-116
 		  2A:3-116
B:3-116

(-) Exons   (0, 0)

(no "Exon" information available for 1ZH4)

(-) 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:121
 aligned with KDPE_ECOLI | P21866 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
           KDPE_ECOLI     1 MTNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHSA 121
               SCOP domains d1zh4a_ A: automated matches                                                                                              SCOP domains
               CATH domains 1zh4A00 A:1-121  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhh...eeee........hhhhhhhhh......eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RESPONSE_REGULATORY  PDB: A:3-116 UniProt: 3-116                                                                  ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zh4 A   1 MTNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHSQ 121
                                    10        20        30        40        50        60        70        80        90       100       110       120 


Chain B from PDB  Type:PROTEIN  Length:120
 aligned with KDPE_ECOLI | P21866 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:120
                                    10        20        30        40        50        60        70        80        90       100       110       120
           KDPE_ECOLI     1 MTNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHS 120
               SCOP domains d1zh4b_ B: automated matches                                                                                             SCOP domains
               CATH domains 1zh4B00 B:1-120  [code=3.40.50.2300, no name defined]                                                                    CATH domains
           Pfam domains (1) ---Response_reg-1zh4B01 B:4-113                                                                                  ------- Pfam domains (1)
           Pfam domains (2) ---Response_reg-1zh4B02 B:4-113                                                                                  ------- Pfam domains (2)
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhh..eeee........hhhhhhhhhhhh...eeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --RESPONSE_REGULATORY  PDB: B:3-116 UniProt: 3-116                                                                  ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zh4 B   1 MTNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRHS 120
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: CheY (97)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KDPE_ECOLI | P21866)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000986    bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0001131    transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BEF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:101 - Pro A:102   [ RasMol ]  
    Lys B:101 - Pro B:102   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1zh4
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  KDPE_ECOLI | P21866
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  KDPE_ECOLI | P21866
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        KDPE_ECOLI | P21866: 1zh2 3zq7 4kfc 4kny 4l85

(-) Related Entries Specified in the PDB File

1zh2 1zh3