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(-) Description

Title :  CRYSTAL STRUCTURE OF D. RADIODURANS BACTERIOPHYTOCHROME PHOTOSENSORY CORE MODULE IN ITS DARK FORM
 
Authors :  H. Takala, J. A. Ihalainen, S. Westenhoff
Date :  14 Dec 13  (Deposition) - 07 May 14  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phytochrome, Red-Light Photoreceptor, Photoconversion, Chromophore, Sensory Transduction, Signaling Protein, Biliverdin, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Takala, A. Bjorling, O. Berntsson, H. Lehtivuori, S. Niebling, M. Hoernke, I. Kosheleva, R. Henning, A. Menzel, J. A. Ihalainen, S. Westenhoff
Signal Amplification And Transduction In Phytochrome Photosensors
Nature V. 509 245 2014
PubMed-ID: 24776794  |  Reference-DOI: 10.1038/NATURE13310

(-) Compounds

Molecule 1 - BACTERIOPHYTOCHROME
    Chains: A, B
    EC Number: 2.7.13.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B(+)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PHOTOSENSORY CORE MODULE, UNP RESIDUES 1-502
    Gene: BPHP
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Strain: R1
    Synonym: PHYTOCHROME-LIKE PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1LBV2Ligand/Ion3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:24 , ILE A:29 , MET A:174 , ASP A:207 , ILE A:208 , TYR A:216 , ARG A:254 , MET A:259 , HIS A:260 , TYR A:263 , MET A:267 , SER A:272 , SER A:274 , HIS A:290BINDING SITE FOR RESIDUE LBV A 600
2AC2SOFTWARECYS B:24 , MET B:174 , TYR B:176 , VAL B:186 , PHE B:203 , SER B:206 , ASP B:207 , ILE B:208 , PRO B:209 , TYR B:216 , ARG B:254 , THR B:256 , SER B:257 , HIS B:260 , TYR B:263 , SER B:272 , LEU B:273 , SER B:274 , HIS B:290BINDING SITE FOR RESIDUE LBV B 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O0P)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:235 -Pro A:236
2Asp B:235 -Pro B:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O0P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O0P)

(-) Exons   (0, 0)

(no "Exon" information available for 4O0P)

(-) 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:485
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.......hhhhh......ee....eeeeee........ee.hhhhhh..hhhhhh..hhhhhh..hhhhhhhhh........eeeeee....eeeeeeee..eeeeeee.....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee............hhhhhhhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhhhh...eeeeeeee..eeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhh.............eeeeee..eeeeee...hhhhhhhhhhhhhhh...eee.hhhhhhhhhh........eeeee....eeeee.....eeeeee.............eeeeee.......hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o0p A   4 DPLPFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWPHLSLTVHRVGELLILEFEPTEAHALRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAADVAAFRQSLREHHARVALAAAHSLSPHDTLSDPALDLLGLMRAGGLILRFEGRWQTLGEVPPAPAVDALLAWLETQPGLVQTDALGQLWPAGADLAPSAAGLLAISVWSECLVWLRPELRLEVAWGGATPDLGPRHSFDTYLEEKRGYAEPWHPGEIEEAQDLRDTLTGALEHHH 506
                                    13        23        33        43        53        63        73        83        93       103  ||   116       126    || 142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       403       413       423      |436       446       456||     471       481       491       501     
                                                                                                                                106|                  131|                                                                                                                                                                                                                                                                   400|                         430|                    457|                                           
                                                                                                                                 110                   138                                                                                                                                                                                                                                                                    402                          434                     463                                           


Chain B from PDB  Type:PROTEIN  Length:484
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.......hhhhh......ee....eeeeee........ee.hhhhhh..hhhhhh..hhhhhh..hhhhhhhhh........eeeeee....eeeeeeee..eeeeeee....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee............hhhhhhhhhhhhhhhh.eeee.......eeee.....................hhhhhhhhhhhh...eeeeeeee..eeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhh.............eeeeee..eeeeee...hhhhhhhhhhhhhhh...eee.hhhhhhhhhh........eeeee.......eeeee.....eeeeee.............eeeeee.......hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o0p B   4 DPLPFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWPHLSLTVHRVGELLILEFEPTEHALRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAADVAAFRQSLREHHARVALAAAHSLSPHDTLSDPALDLLGLMRAGGLILRFEGRWQTLGEVPPAPAVDALLAWLETQPGLVQTDALGQLWPAGADLAPSAAGLLAISVGEGWSECLVWLRPELRLEVAWGGATPDLGPRHSFDTYLEEKRGYAEPWHPGEIEEAQDLRDTLTGALE 503
                                    13        23        33        43        53        63        73        83        93       103  ||   116       126   ||  143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393      |404       414       424       434       444       454  ||   469       479       489       499    
                                                                                                                                106|                 130|                                                                                                                                                                                                                                                                   400|                                                    457|                                        
                                                                                                                                 110                  138                                                                                                                                                                                                                                                                    402                                                     463
   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 4O0P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O0P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O0P)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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  4o0p
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  2.7.13.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        BPHY_DEIRA | Q9RZA4: 1ztu 2o9b 2o9c 3s7n 3s7o 3s7p 3s7q 4cqh 4ijg 4o01 4o8g 4q0h 4q0i 4q0j 4y3i 4y5f 4z1w 4zrr 5ajg 5c5k 5k5b 5l8m 5lbr 5mg0 5mg1

(-) Related Entries Specified in the PDB File

4o01 SAME PHYTOCHROME FRAGMENT BUT IN ILLUMINATED FORM.