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(-) Description

Title :  CRYSTAL STRUCTURE OF D. RADIODURANS BACTERIOPHYTOCHROME PHOTOSENSORY CORE MODULE IN ITS ILLUMINATED FORM
 
Authors :  H. Takala, J. A. Ihalainen, S. Westenhoff
Date :  13 Dec 13  (Deposition) - 07 May 14  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.24
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
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, C, D
    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 R1
    Organism Taxid: 243230
    Strain: R1
    Synonym: PHYTOCHROME-LIKE PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1LBV4Ligand/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
Biological Unit 1 (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
Biological Unit 2 (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  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:24 , PHE A:203 , ASP A:207 , ILE A:208 , PRO A:209 , TYR A:216 , ARG A:254 , THR A:256 , SER A:257 , HIS A:260 , TYR A:263 , SER A:272 , SER A:274 , HIS A:290BINDING SITE FOR RESIDUE LBV A 600
2AC2SOFTWARECYS B:24 , MET B:174 , PHE B:203 , 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 , SER B:274 , HIS B:290BINDING SITE FOR RESIDUE LBV B 600
3AC3SOFTWARECYS C:24 , MET C:174 , PHE C:203 , ASP C:207 , ILE C:208 , PRO C:209 , TYR C:216 , ARG C:222 , ARG C:254 , SER C:257 , MET C:259 , HIS C:260 , TYR C:263 , SER C:272 , SER C:274 , HIS C:290BINDING SITE FOR RESIDUE LBV C 600
4AC4SOFTWARECYS D:24 , MET D:174 , PHE D:203 , ASP D:207 , ILE D:208 , PRO D:209 , TYR D:216 , ARG D:254 , SER D:257 , MET D:259 , HIS D:260 , TYR D:263 , SER D:272 , SER D:274 , HIS D:290 , LEU D:463BINDING SITE FOR RESIDUE LBV D 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O01)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:235 -Pro A:236
2Asp B:235 -Pro B:236
3Asp C:235 -Pro C:236
4Asp D:235 -Pro D:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O01)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O01)

(-) Exons   (0, 0)

(no "Exon" information available for 4O01)

(-) 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:483
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.......hhhhh......ee....eeeeee.....eeeee.hhhhhhh.hhhhhh..hhhhhh.hhhhhhhhhh........eeeee......eeeeeeee..eeeeeeee...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee..ee....ee...........hhhhhhhhhhh...eeeeeeee....eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhh...eeeeee..eeeeee...hhhhhhhhhhhhhhh...eeee.hhhhhhhhhh.......eeeeee.......eeeeee..........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o01 A   6 LPFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWAGHLSLTVHRVGELLILEFEPTEGPHALRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAADVAAFRQSLREHHARVALAAAHSLSPHDTLSDPALDLLGLMRAGGLILRFEGRWQTLGEVPPAPAVDALLAWLETQPGALVQTDALGQLWPAGADLAPSAAGLLAISVGEGWSECLVWLRPELRLEVADLGPRHSFDTYLEEKRGYAEPWHPGEIEEAQDLRDTLTGALEHHH 506
                                    15        25        35        45        55        65        75        85        95       105|      117       127  ||   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       402       412       422       432       442       463       473       483       493       503   
                                                                                                                             105|                   130|                                                                                                                                                                                                                                                                                                                       450|                                            
                                                                                                                              108                    136                                                                                                                                                                                                                                                                                                                        462                                            


Chain B from PDB  Type:PROTEIN  Length:486
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhh.......hhhhh......ee....eeeeee.....eeeee.hhhhhhh.hhhhhh..hhhhhh.hhhhhhhhhh........eeeeeee...eeeeeeeee..eeeeeeee......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee..ee....ee...........hhhhhhhhhhh...eeeeeeee....eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhh...eeeeee..eeeeee...hhhhhhhhhhhhhhh....eee.hhhhhhhhhh.......eeeeee.......eeeeee..........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4o01 B   6 LPFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWAGHLSLTVHRVGELLILEFEPTEWDSGPHALRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAADVAAFRQSLREHHARVALAAAHSLSPHDTLSDPALDLLGLMRAGGLILRFEGRWQTLGEVPPAPAVDALLAWLETQPGALVQTDALGQLWPAGADLAPSAAGLLAISVGEGWSECLVWLRPELRLEVADLGPRHSFDTYLEEKRGYAEPWHPGEIEEAQDLRDTLTGALEHHH 506
                                    15        25        35        45        55        65        75        85        95       105|      117       127  || ||139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449||     470       480       490       500      
                                                                                                                             105|                   130| ||                                                                                                                                                                                                                                                                                                                       450|                                            
                                                                                                                              108                    132 ||                                                                                                                                                                                                                                                                                                                        462                                            
                                                                                                                                                       134|                                                                                                                                                                                                                                                                                                                                                                       
                                                                                                                                                        136                                                                                                                                                                                                                                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:483
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.......hhhhh......ee....eeeeee.....eeeee.hhhhhhh.hhhhhh..hhhhhh.hhhhhhhhhh........eeeeeee...eeeeeeeee..eeeeeeee...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee..ee....ee...........hhhhhhhhhhh...eeeeeeee....eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhh...eeeeee..eeeeee...hhhhhhhhhhhhhhh....eee.hhhhhhhhhh.......eeeeee.......eeeeee..........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o01 C   6 LPFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWAGHLSLTVHRVGELLILEFEPTEGPHALRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAADVAAFRQSLREHHARVALAAAHSLSPHDTLSDPALDLLGLMRAGGLILRFEGRWQTLGEVPPAPAVDALLAWLETQPGALVQTDALGQLWPAGADLAPSAAGLLAISVGEGWSECLVWLRPELRLEVADLGPRHSFDTYLEEKRGYAEPWHPGEIEEAQDLRDTLTGALEHHH 506
                                    15        25        35        45        55        65        75        85        95       105|      117       127  ||   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       402       412       422       432       442       463       473       483       493       503   
                                                                                                                             105|                   130|                                                                                                                                                                                                                                                                                                                       450|                                            
                                                                                                                              108                    136                                                                                                                                                                                                                                                                                                                        462                                            


Chain D from PDB  Type:PROTEIN  Length:482
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.......hhhhh......ee....eeeeee.....eeeee.hhhhhhh.hhhhhh..hhhhhh.hhhhhhhhhh........eeeeeee...eeeeeeeee..eeeeeeee...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..........eehhhhhhhhhhhhhhhh.eeee.......eeee..ee....ee...........hhhhhhhhhhh...eeeeeeee....eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh......hhhhh..eeeeee..eeeeee...hhhhhhhhhhhhhhh....eee.hhhhhhhhhh.......eeeeee.......eeeeee.........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o01 D   6 LPFFPPLYLGGPEITTENCEREPIHIPGSIQPHGALLTADGHSGEVLQMSLNAATFLGQEPTVLRGQTLAALLPEQWPALQAALPPGCPDALQYRATLDWAGHLSLTVHRVGELLILEFEPTEGPHALRNAMFALESAPNLRALAEVATQTVRELTGFDRVMLYKFAPDATGEVIAEARREGLHAFLGHRFPASDIPAQARALYTRHLLRLTADTRAAAVPLDPVLNPQTNAPTPLGGAVLRATSPMHMQYLRNMGVGSSLSVSVVVGGQLWGLIACHHQTPYVLPPDLRTTLEYLGRLLSLQVQVKEAADVAAFRQSLREHHARVALAAAHSLSPHDTLSDPALDLLGLMRAGGLILRFEGRWQTLGEVPPAPAVDALLAWLETQPGALVQTDALGQLWPAGADLAPSAAGLLAISVGEGWSECLVWLRPELRLEVALGPRHSFDTYLEEKRGYAEPWHPGEIEEAQDLRDTLTGALEHHH 506
                                    15        25        35        45        55        65        75        85        95       105|      117       127  ||   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       402       412       422       432       442       464       474       484       494       504  
                                                                                                                             105|                   130|                                                                                                                                                                                                                                                                                                                       450|                                           
                                                                                                                              108                    136                                                                                                                                                                                                                                                                                                                        463
   Legend:   → Mismatch (orange background)
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  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 4O01)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O01)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O01)

(-) Gene Ontology  (18, 18)

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  4o01
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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 4o0p 4o8g 4q0h 4q0i 4q0j 4y3i 4y5f 4z1w 4zrr 5ajg 5c5k 5k5b 5l8m 5lbr 5mg0 5mg1

(-) Related Entries Specified in the PDB File

4o0p