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(-) Description

Title :  STRUCTURE OF A BLUE-LIGHT PHOTORECEPTOR
 
Authors :  R. P. Diensthuber, M. Bommer, A. Moglich
Date :  31 Jul 12  (Deposition) - 19 Jun 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Photoreceptor, Signal Transduction, Two-Component System, Light- Oxygen-Voltage, Per-Arnt-Sim, Dhp, Sensor Histidine Kinase, Signaling Protein, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. P. Diensthuber, M. Bommer, T. Gleichmann, A. Moglich
Full-Length Structure Of A Sensor Histidine Kinase Pinpoint Coaxial Coiled Coils As Signal Transducers And Modulators.
Structure V. 21 1127 2013
PubMed-ID: 23746806  |  Reference-DOI: 10.1016/J.STR.2013.04.024

(-) Compounds

Molecule 1 - BLUE-LIGHT PHOTORECEPTOR, SENSOR PROTEIN FIXL
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET41
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP O34627 RESIDUES 1-126, UNP P23222 RESIDUES 257-505
    Gene: PFYP, YTVA, BSU30340, FIXL, BLL2760
    Organism Scientific: BACILLUS SUBTILIS, BRADYRHIZOBIUM JAPONICUM
    Organism Taxid: 224308, 224911
    Strain: 168, USDA 110
    Synonym: PHOTOACTIVE FLAVO-YELLOW PROTEIN, PHOTOTROPIN HOMOLOG

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 33)

Asymmetric/Biological Unit (4, 33)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3MSE20Mod. Amino AcidSELENOMETHIONINE
4SO410Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:28 , THR A:30 , ASN A:37 , ASN A:61 , CYS A:62 , ARG A:63 , LEU A:65 , GLN A:66 , ILE A:78 , ARG A:79 , LEU A:82 , ASN A:94 , ASN A:104 , LEU A:106 , ILE A:108 , PHE A:119 , GLY A:121 , GLN A:123 , HOH A:531 , HOH A:533 , HOH A:534BINDING SITE FOR RESIDUE FMN A 401
02AC2SOFTWAREASN A:275 , ASN A:279 , ALA A:283 , ASP A:310 , GLY A:314 , PHE A:315 , LEU A:323 , PHE A:328 , THR A:329 , THR A:330 , LYS A:331 , MSE A:335 , GLY A:336 , GLY A:338 , LEU A:339 , ALA A:363 , PHE A:365 , HOH A:501 , HOH A:509 , HOH A:570 , HOH A:602 , HOH A:606 , HOH A:610 , HOH A:616 , HOH A:725BINDING SITE FOR RESIDUE ADP A 402
03AC3SOFTWAREHIS A:161 , ARG A:211 , ARG A:214BINDING SITE FOR RESIDUE SO4 A 403
04AC4SOFTWARELYS A:17 , SER B:3 , GLY B:8 , ILE B:9BINDING SITE FOR RESIDUE SO4 A 404
05AC5SOFTWAREGLY A:243 , ALA A:244 , ARG A:245 , GLU A:246 , HOH B:581BINDING SITE FOR RESIDUE SO4 A 405
06AC6SOFTWAREPHE A:324 , ARG A:343 , HOH A:507 , HOH A:541 , HOH A:747BINDING SITE FOR RESIDUE SO4 A 406
07AC7SOFTWAREVAL B:28 , THR B:30 , ASN B:37 , ASN B:61 , CYS B:62 , ARG B:63 , GLN B:66 , VAL B:75 , ARG B:79 , LEU B:82 , ASN B:94 , ASN B:104 , LEU B:106 , ILE B:108 , PHE B:119 , GLY B:121 , GLN B:123BINDING SITE FOR RESIDUE FMN B 401
08AC8SOFTWAREHIS B:161 , ASN B:164 , ARG B:214 , HOH B:605BINDING SITE FOR RESIDUE SO4 B 402
09AC9SOFTWAREHIS A:129 , HIS B:129 , HOH B:532BINDING SITE FOR RESIDUE SO4 B 403
10BC1SOFTWAREVAL A:337 , SER B:147 , SER B:150 , ALA B:151 , GLU B:154 , HOH B:582BINDING SITE FOR RESIDUE SO4 B 404
11BC2SOFTWAREARG A:245 , GLN A:250 , ARG A:252 , HIS B:378BINDING SITE FOR RESIDUE SO4 B 405
12BC3SOFTWAREARG A:148 , SER B:222 , LYS B:224 , GLN B:268BINDING SITE FOR RESIDUE SO4 B 406
13BC4SOFTWAREPHE B:119 , HOH B:587BINDING SITE FOR RESIDUE SO4 B 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GCZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GCZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GCZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GCZ)

(-) Exons   (0, 0)

(no "Exon" information available for 4GCZ)

(-) 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:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....eeeee........eeeehhhhhhhhh.hhhhh...hhhhhh....hhhhhhhhhhhhhh...eeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeehhhhhhhhhhhhh........eeeee.hhhh.eeeehhhhhhhhhhhhhhhhhhhh......eeeeeeeee...eeeeeee.........hhhhh.............hhhhhhhhhhhhh...eeeee.....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gcz A   8 GIPGQLEVIKKALDHVRVGVVITDPALEDNPIVYVNQGFVQmTGYETEEILGKNCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNYKKDGTmFWNELNIDPmEIEDKTYFVGIQNDITEHQQTQARLQELQSELVHVSRLSAmGEmASALAHELNQPLAAISNYmKGSRRLLAGSSDPNTPKVESALDRAAEQALRAGQIIRRLRDFVARGESEKRVESLSKLIEEAGALGLAGAREQNVQLRFSLDPGADLVLADRVQIQQVLVNLFRNALEAmAQSQRRELVVTNTPAADDmIEVEVSDTGSGFQDDVIPNLFQTFFTTKDTGmGVGLSISRSIIEAHGGRmWAESNASGGATFRFTLPAAD 373
                                    17        27        37        47 |      57        67        77        87        97   |   107   |   117       127       137       147    |  157       167      |177       187       197       207       217       227       237       247       257       267       277      |287       297     | 307       317       327       337       347     | 357       367      
                                                                    49-MSE                                             101-MSE   111-MSE                                  152-MSE               174-MSE                                                                                                       284-MSE            303-MSE                         335-MSE           353-MSE                
                                                                                                                                                                             155-MSE                                                                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:378
                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh..eeeee........eeeehhhhhhhhh.hhhhh...hhhhhh....hhhhhhhhhhhhhh...eeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeehhhhhhhhhhhhh........eeeee......eeeehhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee...eeeeeee.........eee......eee..hhhhhhhhhhhhhhhhh...eeeee.....eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gcz B   2 ASFQSFGIPGQLEVIKKALDHVRVGVVITDPALEDNPIVYVNQGFVQmTGYETEEILGKNCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNYKKDGTmFWNELNIDPmEIEDKTYFVGIQNDITEHQQTQARLQELQSELVHVSRLSAmGEmASALAHELNQPLAAISNYmKGSRRLLAGSSDPNTPKVESALDRAAEQALRAGQIIRRLRDFVAGESEKRVESLSKLIEEAGALGLAGAREQNVQLRFSLDPGADLVLADRVQIQQVLVNLFRNALEAmAQSQRRELVVTNTPAADDmIEVEVSDTGSGFQDDVIPNLFQTFFTTKDTGmGVGLSISRSIIEAHGGRmWAESNASGGATFRFTLPAADENLEHHH 380
                                    11        21        31        41       |51        61        71        81        91       101       111       121       131       141       151|  |   161       171  |    181       191       201       211      |222       232       242       252       262       272       282 |     292       302|      312       322       332  |    342       352|      362       372        
                                                                          49-MSE                                             101-MSE   111-MSE                                  152-MSE               174-MSE                                     218|                                                             284-MSE            303-MSE                         335-MSE           353-MSE                       
                                                                                                                                                                                   155-MSE                                                         220
   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  (0, 0)

(no "SCOP Domain" information available for 4GCZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GCZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GCZ)

(-) Gene Ontology  (20, 25)

Asymmetric/Biological Unit(hide GO term definitions)

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  4gcz
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  FIXL_BRADU | P23222
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 Related Entries

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

UniProtKB/Swiss-Prot
        FIXL_BRADU | P23222: 1dp6 1dp8 1dp9 1drm 1lsv 1lsw 1lsx 1lt0 1xj2 1xj3 1xj4 1xj6 1y28 2cmn 2owh 2owj 2vv6 2vv7 2vv8
        PHOT_BACSU | O34627: 1ium 2mwg 2pr5 2pr6

(-) Related Entries Specified in the PDB File

2pr5