Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  SENSOR REGION OF A SENSOR HISTIDINE KINASE
 
Authors :  J. Preu, S. Panjikar, P. Morth, R. Jaiswal, P. Karunakar, P. A. Tucker
Date :  26 May 11  (Deposition) - 06 Jun 12  (Release) - 23 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Two-Component System, Gaf Domain, Pas Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Preu, S. Panjikar, P. Morth, R. Jaiswal, P. Karunakar, P. A. Tucker
The Sensor Region Of The Ubiquitous Cytosolic Sensor Kinase Pdtas, Contains Pas And Gaf Domain Sensing Modules.
J. Struct. Biol. V. 177 498 2012
PubMed-ID: 22115998  |  Reference-DOI: 10.1016/J.JSB.2011.11.012

(-) Compounds

Molecule 1 - PROBABLE SENSOR HISTIDINE KINASE PDTAS
    Chains: A
    EC Number: 2.7.13.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM11RV3320CN-TERM
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: CC1
    Expression System Vector Type: PLASMID
    Fragment: GAF AND PAS DOMAINS, RESIDUES 1-303
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: PDTAS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1BR16Ligand/IonBROMIDE ION
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:59 , ASN A:60 , THR A:61 , GLY A:62 , ARG A:137 , LEU A:142 , TYR A:146 , GLY A:178 , BR A:1294BINDING SITE FOR RESIDUE SO4 A1287
02AC2SOFTWAREASN A:60 , HOH A:2020 , HOH A:2038BINDING SITE FOR RESIDUE BR A1288
03AC3SOFTWARELEU A:142 , ASN A:196BINDING SITE FOR RESIDUE BR A1289
04AC4SOFTWAREASP A:69BINDING SITE FOR RESIDUE BR A1290
05AC5SOFTWAREMET A:80 , LEU A:82BINDING SITE FOR RESIDUE BR A1291
06AC6SOFTWARELEU A:210 , GLU A:211 , HOH A:2103BINDING SITE FOR RESIDUE BR A1292
07AC7SOFTWAREHOH A:2014BINDING SITE FOR RESIDUE BR A1293
08AC8SOFTWARETHR A:64 , LEU A:142 , SO4 A:1287BINDING SITE FOR RESIDUE BR A1294
09AC9SOFTWAREARG A:172 , SER A:173BINDING SITE FOR RESIDUE BR A1295
10BC1SOFTWAREBR A:1297BINDING SITE FOR RESIDUE BR A1296
11BC2SOFTWAREPRO A:221 , BR A:1296BINDING SITE FOR RESIDUE BR A1297
12BC3SOFTWAREMET A:247 , ARG A:248BINDING SITE FOR RESIDUE BR A1298
13BC4SOFTWAREGLU A:132BINDING SITE FOR RESIDUE BR A1299
14BC5SOFTWAREHOH A:2092BINDING SITE FOR RESIDUE BR A1300
15BC6SOFTWAREHIS A:67 , THR A:68BINDING SITE FOR RESIDUE BR A1301
16BC7SOFTWAREHOH A:2070 , HOH A:2093BINDING SITE FOR RESIDUE BR A1302
17BC8SOFTWARESER A:224 , GLY A:255 , HOH A:2124BINDING SITE FOR RESIDUE BR A1303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:162 -Pro A:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YKF)

(-) 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:263
 aligned with PDTAS_MYCTO | P9WGL4 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:286
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280      
          PDTAS_MYCTO     1 MSTLGDLLAEHTVLPGSAVDHLHAVVGEWQLLADLSFADYLMWVRRDDGVLVCVAQCRPNTGPTVVHTDAVGTVVAANSMPLVAATFSGGVPGREGAVGQQNSCQHDGHSVEVSPVRFGDQVVAVLTRHQPELAARRRSGHLETAYRLCATDLLRMLAEGTFPDAGDVAMSRSSPRAGDGFIRLDVDGVVSYASPNALSAYHRMGLTTELEGVNLIDATRPLISDPFEAHEVDEHVQDLLAGDGKGMRMEVDAGGATVLLRTLPLVVAGRNVGAAILIRDVTEVKR 286
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....eeeeeee................eehhhhhhhhhhhhhh.------------------...eeeeeee..eeeeeeeee..hhhhh...hhhhhhhhhhhhhhhhhhhh......-----.....hhhh.eeee.....eeeehhhhhhhhhhh.........hhhhhhh....hhhhhhhhhhhhhhhhh......eeeeee..eeeeeeeeeeee..eeeeeeeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ykf A   1 MSTLGDLLAEHTVLPGSAVDHLHAVVGEWQLLADLSFADYLMWVRRDDGVLVCVAQCRPNTGPTVVHTDAVGTVVAANSMPLVAATFSGG------------------HSVEVSPVRFGDQVVAVLTRHQPELAARRRSGHLETAYRLCATDLLRMLAEGTFPDA-----SRSSPRAGDGFIRLDVDGVVSYASPNALSAYHRMGLTTELEGVNLIDATRPLISDPFEAHEVDEHVQDLLAGDGKGMRMEVDAGGATVLLRTLPLVVAGRNVGAAILIRDVTEVKR 286
                                    10        20        30        40        50        60        70        80        90         -       110       120       130       140       150       160    |    -|      180       190       200       210       220       230       240       250       260       270       280      
                                                                                                                    90                109                                                     165   171                                                                                                                   


Chain A from PDB  Type:PROTEIN  Length:263
 aligned with PDTAS_MYCTU | P9WGL5 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:286
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280      
          PDTAS_MYCTU     1 MSTLGDLLAEHTVLPGSAVDHLHAVVGEWQLLADLSFADYLMWVRRDDGVLVCVAQCRPNTGPTVVHTDAVGTVVAANSMPLVAATFSGGVPGREGAVGQQNSCQHDGHSVEVSPVRFGDQVVAVLTRHQPELAARRRSGHLETAYRLCATDLLRMLAEGTFPDAGDVAMSRSSPRAGDGFIRLDVDGVVSYASPNALSAYHRMGLTTELEGVNLIDATRPLISDPFEAHEVDEHVQDLLAGDGKGMRMEVDAGGATVLLRTLPLVVAGRNVGAAILIRDVTEVKR 286
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....eeeeeee................eehhhhhhhhhhhhhh.------------------...eeeeeee..eeeeeeeee..hhhhh...hhhhhhhhhhhhhhhhhhhh......-----.....hhhh.eeee.....eeeehhhhhhhhhhh.........hhhhhhh....hhhhhhhhhhhhhhhhh......eeeeee..eeeeeeeeeeee..eeeeeeeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ykf A   1 MSTLGDLLAEHTVLPGSAVDHLHAVVGEWQLLADLSFADYLMWVRRDDGVLVCVAQCRPNTGPTVVHTDAVGTVVAANSMPLVAATFSGG------------------HSVEVSPVRFGDQVVAVLTRHQPELAARRRSGHLETAYRLCATDLLRMLAEGTFPDA-----SRSSPRAGDGFIRLDVDGVVSYASPNALSAYHRMGLTTELEGVNLIDATRPLISDPFEAHEVDEHVQDLLAGDGKGMRMEVDAGGATVLLRTLPLVVAGRNVGAAILIRDVTEVKR 286
                                    10        20        30        40        50        60        70        80        90         -       110       120       130       140       150       160    |    -|      180       190       200       210       220       230       240       250       260       270       280      
                                                                                                                    90                109                                                     165   171
   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 2YKF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (PDTAS_MYCTU | P9WGL5)
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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    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: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:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    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: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.

Chain A   (PDTAS_MYCTO | P9WGL4)
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: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.
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.
cellular component
    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.

 Visualization

(-) Interactive Views

Asymmetric 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
    BR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:162 - Pro A:163   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  2ykf
    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
  PDTAS_MYCTO | P9WGL4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PDTAS_MYCTU | P9WGL5
    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)
  2.7.13.3
    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
  PDTAS_MYCTO | P9WGL4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PDTAS_MYCTU | P9WGL5
    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
        PDTAS_MYCTO | P9WGL4: 2ykh
        PDTAS_MYCTU | P9WGL5: 2ykh

(-) Related Entries Specified in the PDB File

2ykh SENSOR REGION OF A SENSOR HISTIDINE KINASE