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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEIN DOMAIN FROM THE SENSOR HISTIDINE KINASE PPR FROM RHODOSPIRILLUM CENTENUM
 
Authors :  S. Rajagopal, K. Moffat
Date :  09 Oct 02  (Deposition) - 25 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Photoactive Yellow Protein, Pas, Pyp, Ppr, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Rajagopal, K. Moffat
Crystal Structure Of A Photoactive Yellow Protein From A Sensor Histidine Kinase: Conformational Variability And Signal Transduction
Proc. Natl. Acad. Sci. Usa V. 100 1649 2003
PubMed-ID: 12563032  |  Reference-DOI: 10.1073/PNAS.0336353100
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PPR
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentN-TERMINAL DOMAIN
    Organism ScientificRHODOSPIRILLUM CENTENUM
    Organism Taxid34018

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1HC43Ligand/Ion4'-HYDROXYCINNAMIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HC41Ligand/Ion4'-HYDROXYCINNAMIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HC41Ligand/Ion4'-HYDROXYCINNAMIC ACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1HC41Ligand/Ion4'-HYDROXYCINNAMIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:42 , GLU A:46 , SER A:50 , ALA A:67 , PRO A:68 , CYS A:69 , PHE A:98BINDING SITE FOR RESIDUE HC4 A 130
2AC2SOFTWARETYR B:42 , GLU B:46 , SER B:50 , ALA B:67 , PRO B:68 , CYS B:69 , PHE B:98 , ALA C:25BINDING SITE FOR RESIDUE HC4 B 130
3AC3SOFTWAREALA A:25 , TYR C:42 , GLU C:46 , SER C:50 , VAL C:66 , ALA C:67 , PRO C:68 , CYS C:69BINDING SITE FOR RESIDUE HC4 C 130

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MZU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MZU)

(-) 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:107
 aligned with Q9X2W8_RHOCE | Q9X2W8 from UniProtKB/TrEMBL  Length:884

    Alignment length:110
                                    29        39        49        59        69        79        89        99       109       119       129
         Q9X2W8_RHOCE    20 IDGMGTAEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGTLDARFDFVFDFQMAPVRVQIRMQNAGVPDRYWIFVRK 129
               SCOP domains d1   mzua_ A: PYP domain of sensor histidine kinase Ppr                                                        SCOP domains
               CATH domains 1m   zuA00 A:15-124  [code=3.30.450.20, no name defined]                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..---..hhhhh..eeeeee....eeeehhhhhhhhh.hhhhhh........hhhhh...hhhhhhhhhhh...eeeeeeeee....eeeeeeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1mzu A  15 ID---TAEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGTLDARFDFVFDFQMAPVRVQIRMQNAGVPDRYWIFVRK 124
                             |   |  24        34        44        54        64        74        84        94       104       114       124
                             |  20                                                                                                        
                            16                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with Q9X2W8_RHOCE | Q9X2W8 from UniProtKB/TrEMBL  Length:884

    Alignment length:114
                                    25        35        45        55        65        75        85        95       105       115       125    
         Q9X2W8_RHOCE    16 IRGTIDGMGTAEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGTLDARFDFVFDFQMAPVRVQIRMQNAGVPDRYWIFVRK 129
               SCOP domains d1mzub_ B: PYP domain of sensor histidine kinase Ppr                                                               SCOP domains
               CATH domains 1mzuB00 B:11-124  [code=3.30.450.20, no name defined]                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhh....eeeeee....eeeehhhhhhhhh.hhhhhh........hhhhh...hhhhhhhhhhhh..eeeeeeee......eeeeeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1mzu B  11 IRGTIDGMGTAEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGTLDARFDFVFDFQMAPVRVQIRMQNAGVPDRYWIFVRK 124
                                    20        30        40        50        60        70        80        90       100       110       120    

Chain C from PDB  Type:PROTEIN  Length:108
 aligned with Q9X2W8_RHOCE | Q9X2W8 from UniProtKB/TrEMBL  Length:884

    Alignment length:114
                                    25        35        45        55        65        75        85        95       105       115       125    
         Q9X2W8_RHOCE    16 IRGTIDGMGTAEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGTLDARFDFVFDFQMAPVRVQIRMQNAGVPDRYWIFVRK 129
               SCOP domains d1mzuc_ C: PYP domain of sensor histidine kinase Ppr                                                               SCOP domains
               CATH domains 1mzuC00 C:11-124  [code=3.30.450.20, no name defined]                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...eeeee.....eeeehhhhhhhhh.hhhhhh........hhhhh...hhhhhhhhhh....eeeeee.------...eeeeeee......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1mzu C  11 IRGTIDGMGTAEFDALPVGAIQVDGSGVIHRYNRTESRLSGRIPERVIGRNFFTEVAPCTNIPAFSGRFMDGVTSGTLDARFDFV------PVRVQIRMQNAGVPDRYWIFVRK 124
                                    20        30        40        50        60        70        80        90    |    - |     110       120    
                                                                                                               95    102                      

   Legend:   → Mismatch (orange background)
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    → 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, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q9X2W8_RHOCE | Q9X2W8)
molecular function
    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:0009881    photoreceptor activity    The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
biological process
    GO:0009584    detection of visible light    The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm.
    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:0007602    phototransduction    The sequence of reactions within a cell required to convert absorbed photons into a molecular signal.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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: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.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1g28 FLAVIN-BINDING DOMAIN, LOV2, FROM THE CHIMERIC PHYTOCHROME/ PHOTOTROPIN PHOTORECEPTOR PHY3
1gsv THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN G47S MUTANT
2phy PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED)
2pyp PHOTOACTIVE YELLOW PROTEIN, PHOTOSTATIONARY STATE, 50% GROUND STATE, 50% BLEACHED