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(-) Description

Title :  DARK STATE STRUCTURE OF THE BLUF DOMAIN OF THE RHODOBACTERIAL PROTEIN APPA
 
Authors :  A. Jung, J. Reinstein, T. Domratcheva, R. -L. Shoeman, I. Schlichting
Date :  17 Jul 06  (Deposition) - 06 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Signal Transduction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Jung, J. Reinstein, T. Domratcheva, R. -L. Shoeman, I. Schlichting
Crystal Structures Of The Appa Bluf Domain Photoreceptor Provide Insights Into Blue Light- Mediated Signal Transduction.
J. Mol. Biol. V. 362 717 2006
PubMed-ID: 16949615  |  Reference-DOI: 10.1016/J.JMB.2006.07.024

(-) Compounds

Molecule 1 - APPA, ANTIREPRESSOR OF PPSR, SENSOR OF BLUE LIGHT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: BLUF DOMAIN, RESIDUES 1-124
    Mutation: YES
    Organism Scientific: RHODOBACTER SPHAEROIDES
    Organism Taxid: 1063

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2DTU1Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2DTU2Ligand/Ion(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3FMN4Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:21 , ILE A:37 , THR A:40 , SER A:41 , HIS A:44 , ASN A:45 , PHE A:61 , GLN A:63 , LEU A:65 , VAL A:75 , HIS A:78 , ILE A:79 , ASP A:82 , ARG A:84 , HIS A:85 , HOH A:2029 , LYS B:98BINDING SITE FOR RESIDUE FMN A1122
2AC2SOFTWARECYS A:19 , MET A:76 , ILE A:90 , LEU A:91 , GLU A:93BINDING SITE FOR RESIDUE DTU A1123
3AC3SOFTWARETYR B:21 , ILE B:37 , THR B:40 , SER B:41 , HIS B:44 , ASN B:45 , PHE B:61 , GLN B:63 , HIS B:78 , ILE B:79 , ASP B:82 , ARG B:84 , HIS B:85 , MET B:106 , HOH B:2030 , HOH B:2031BINDING SITE FOR RESIDUE FMN B1122
4AC4SOFTWARECYS B:19 , ALA B:70 , ALA B:73 , MET B:76 , LEU B:91 , GLU B:93BINDING SITE FOR RESIDUE DTT B1123

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IYG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IYG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IYG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IYG)

(-) Exons   (0, 0)

(no "Exon" information available for 2IYG)

(-) 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:109
 aligned with Q3J677_RHOS4 | Q3J677 from UniProtKB/TrEMBL  Length:450

    Alignment length:109
                                    22        32        42        52        62        72        82        92       102       112         
         Q3J677_RHOS4    13 GSDLVSCCYRSLAAPDLTLRDLLDIVETSQAHNARAQLTGALFYSQGVFFQWLEGRPAAVAEVMTHIQRDRRHSNVEILAEEPIAKRRFAGWHMQLSCSEADMRSLGLA 121
               SCOP domains d2iyga_ A: automated matches                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeeeehhhhhhhhhhhhhhh..eeeeeeeeeee...........eee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2iyg A  13 GSDLVSCSYRSLAAPDLTLRDLLDIVETSQAHNARAQLTGALFYSQGVFFQWLEGRPAAVAEVMTHIQRDRRHSNVEILAEEPIAKRRFAGWHMQLSCSEADMRSLGLA 121
                                    22        32        42        52        62        72        82        92       102       112         


Chain B from PDB  Type:PROTEIN  Length:108
 aligned with Q3J677_RHOS4 | Q3J677 from UniProtKB/TrEMBL  Length:450

    Alignment length:108
                                    23        33        43        53        63        73        83        93       103       113        
         Q3J677_RHOS4    14 SDLVSCCYRSLAAPDLTLRDLLDIVETSQAHNARAQLTGALFYSQGVFFQWLEGRPAAVAEVMTHIQRDRRHSNVEILAEEPIAKRRFAGWHMQLSCSEADMRSLGLA 121
               SCOP domains d2iygb_ B: automated matches                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeeeeehhhhhhhhhhhhhh...eeeeeeeeeeee..........eee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2iyg B  14 SDLVSCSYRSLAAPDLTLRDLLDIVETSQAHNARAQLTGALFYSQGVFFQWLEGRPAAVAEVMTHIQRDRRHSNVEILAEEPIAKRRFAGWHMQLSCSEADMRSLGLA 121
                                    23        33        43        53        63        73        83        93       103       113
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2IYG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IYG)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q3J677_RHOS4 | Q3J677)
molecular function
    GO:0071949    FAD binding    Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0009882    blue light photoreceptor activity    The function of absorbing and responding to electromagnetic radiation with a wavelength of approximately 400-470nm. The response may involve a change in conformation.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0009785    blue light signaling pathway    The series of molecular signals initiated upon sensing of blue light by photoreceptor molecule, at a wavelength between 400nm and 470nm.

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  2iyg
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 Related Entries

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

UniProtKB/TrEMBL
        Q3J677_RHOS4 | Q3J677: 2iyi

(-) Related Entries Specified in the PDB File

1x0p STRUCTURE OF A CYANOBACTERIAL BLUF PROTEIN, TLL0078
1yrx STRUCTURE OF A NOVEL PHOTORECEPTOR: THE BLUF DOMAIN OF APPAFROM RHODOBACTER SPHAEROIDES
2bun SOLUTION STRUCTURE OF THE BLUF DOMAIN OF APPA 5-125
2byc BLRB - A BLUF PROTEIN, DARK STATE STRUCTUREA
2iyi STRUCTURE OF A LIGHT-INDUCED INTERMEDIATE OF THE BLUF DOMAIN OF THE RHODOBACTERIAL PROTEIN APPA