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(-) Description

Title :  CRYSTAL STRUCTURE OF HEMAT SENSOR DOMAIN FROM B.SUBTILIS IN THE CYANO-LIGANDED FORM
 
Authors :  W. Zhang, G. N. Phillips Jr.
Date :  11 Mar 03  (Deposition) - 23 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Globin Fold, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Zhang, G. N. Phillips
Structure Of The Oxygen Sensor In Bacillus Subtilis: Signal Transduction Of Chemotaxis By Control Of Symmetry.
Structure V. 11 1097 2003
PubMed-ID: 12962628  |  Reference-DOI: 10.1016/S0969-2126(03)00169-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEME-BASED AEROTACTIC TRANSDUCER HEMAT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET29
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YHFV
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 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
1CYN2Ligand/IonCYANIDE ION
2HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:70 , LEU A:92 , HIS A:123 , HEM A:180BINDING SITE FOR RESIDUE CYN A 181
2AC2SOFTWARETYR B:70 , HIS B:123 , HEM B:180 , HOH B:182BINDING SITE FOR RESIDUE CYN B 181
3AC3SOFTWAREPHE A:69 , LEU A:79 , ILE A:82 , HIS A:86 , HIS A:99 , ILE A:119 , HIS A:123 , ILE A:126 , LEU A:128 , PHE A:137 , CYN A:181 , HOH A:265BINDING SITE FOR RESIDUE HEM A 180
4AC4SOFTWARESER A:15 , SER A:17 , GLN A:20 , LEU B:73 , LEU B:79 , ILE B:83 , SER B:87 , LEU B:92 , LEU B:96 , HIS B:99 , ILE B:119 , HIS B:123 , ILE B:126 , LEU B:128 , PHE B:137 , LEU B:140 , CYN B:181BINDING SITE FOR RESIDUE HEM B 180

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OR4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:177 -Glu A:178

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OR4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OR4)

(-) Exons   (0, 0)

(no "Exon" information available for 1OR4)

(-) 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:169
 aligned with HEMAT_BACSU | O07621 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:169
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
          HEMAT_BACSU    10 ETAYFSDSNGQQKNRIQLTNKHADVKKQLKMVRLGDAELYVLEQLQPLIQENIVNIVDAFYKNLDHESSLMDIINDHSSVDRLKQTLKRHIQEMFAGVIDDEFIEKRNRIASIHLRIGLLPKWYMGAFQELLLSMIDIYEASITNQQELLKAIKATTKILNLEQQLVLE 178
               SCOP domains d1or4a_ A: Heme-based aerotactic transducer HemAT, sensor domain                                                                                                          SCOP domains
               CATH domains 1or4A00 A:10-178 Globins                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh..ee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1or4 A  10 ETAYFSDSNGQQKNRIQLTNKHADVKKQLKMVRLGDAELYVLEQLQPLIQENIVNIVDAFYKNLDHESSLMDIINDHSSVDRLKQTLKRHIQEMFAGVIDDEFIEKRNRIASIHLRIGLLPKWYMGAFQELLLSMIDIYEASITNQQELLKAIKATTKILNLEQQLVLE 178
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         


Chain B from PDB  Type:PROTEIN  Length:158
 aligned with HEMAT_BACSU | O07621 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:158
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
          HEMAT_BACSU    21 QKNRIQLTNKHADVKKQLKMVRLGDAELYVLEQLQPLIQENIVNIVDAFYKNLDHESSLMDIINDHSSVDRLKQTLKRHIQEMFAGVIDDEFIEKRNRIASIHLRIGLLPKWYMGAFQELLLSMIDIYEASITNQQELLKAIKATTKILNLEQQLVLE 178
               SCOP domains d1or4b_ B: Heme-based aerotactic transducer HemAT, sensor domain                                                                                               SCOP domains
               CATH domains 1or4B00 B:21-178 Globins                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1or4 B  21 QKNRIQLTNKHADVKKQLKMVRLGDAELYVLEQLQPLIQENIVNIVDAFYKNLDHESSLMDIINDHSSVDRLKQTLKRHIQEMFAGVIDDEFIEKRNRIASIHLRIGLLPKWYMGAFQELLLSMIDIYEASITNQQELLKAIKATTKILNLEQQLVLE 178
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1OR4)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HEMAT_BACSU | O07621)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0009454    aerotaxis    The directed movement of a motile cell or organism in response to environmental oxygen.
    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.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        HEMAT_BACSU | O07621: 1or6

(-) Related Entries Specified in the PDB File

1or6