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(-) Description

Title :  CRYSTAL STRUCTURE OF CYANOBACTERIOCHROME TEPIXJ GAF DOMAIN
 
Authors :  T. Ishizuka, R. Narikawa, N. Muraki, T. Shiba, G. Kurisu, M. Ikeuchi
Date :  14 Jul 12  (Deposition) - 30 Jan 13  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Cyanobacteriochrome, Phycoviolobilin Binding, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Narikawa, T. Ishizuka, N. Muraki, T. Shiba, G. Kurisu, M. Ikeuchi
Structures Of Cyanobacteriochromes From Phototaxis Regulators Anpixj And Tepixj Reveal General And Specific Photoconversion Mechanism
Proc. Natl. Acad. Sci. Usa V. 110 918 2013
PubMed-ID: 23256156  |  Reference-DOI: 10.1073/PNAS.1212098110

(-) Compounds

Molecule 1 - METHYL-ACCEPTING CHEMOTAXIS PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: SYNECHOCYSTIS
    Expression System Strain: PCC6803
    Expression System Taxid: 1148
    Fragment: GAF DOMAIN, UNP RESIDUES 430-591
    Gene: TLL0569
    Organism Scientific: THERMOSYNECHOCOCCUS ELONGATUS
    Organism Taxid: 197221
    Strain: BP-1
    Synonym: TEPIXJ

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1PVG2Ligand/IonPHYCOVIOLOBILIN, GREEN LIGHT-ABSORBING FORM
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1PVG1Ligand/IonPHYCOVIOLOBILIN, GREEN LIGHT-ABSORBING FORM
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1PVG1Ligand/IonPHYCOVIOLOBILIN, GREEN LIGHT-ABSORBING FORM
2SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:35 , VAL A:45 , GLU A:63 , ASP A:64 , PRO A:65 , GLU A:69 , TRP A:71 , ARG A:79 , GLN A:81 , CYS A:94 , HIS A:95 , GLN A:98 , ASN A:107 , HOH A:311 , HOH A:319 , HOH A:321 , HOH A:334 , HOH A:351 , HOH A:361BINDING SITE FOR RESIDUE PVG A 201
2AC2SOFTWAREARG A:24 , GLU A:52BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWARETHR A:84 , GLN A:132BINDING SITE FOR RESIDUE SO4 A 203
4AC4SOFTWAREARG A:105BINDING SITE FOR RESIDUE SO4 A 204
5AC5SOFTWAREILE B:33 , TYR B:35 , VAL B:45 , ILE B:62 , GLU B:63 , ASP B:64 , PRO B:65 , GLU B:69 , TRP B:71 , ARG B:79 , GLN B:81 , CYS B:94 , HIS B:95 , GLN B:98 , LEU B:102 , ASN B:107 , HOH B:307 , HOH B:309 , HOH B:316BINDING SITE FOR RESIDUE PVG B 201
6AC6SOFTWAREARG B:24 , ALA B:51 , GLU B:52BINDING SITE FOR RESIDUE SO4 B 202

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:66 -B:66

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VV4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VV4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VV4)

(-) Exons   (0, 0)

(no "Exon" information available for 3VV4)

(-) 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:153
 aligned with Q8DLC7_THEEB | Q8DLC7 from UniProtKB/TrEMBL  Length:940

    Alignment length:153
                                   443       453       463       473       483       493       503       513       523       533       543       553       563       573       583   
         Q8DLC7_THEEB   434 LSELRDRQAIFETLVAKGRELLACDRVIVYAFDDNYVGTVVAESVAEGWPQARDQVIEDPCFREHWVEAYRQGRIQATTDIFKAGLTECHLNQLRPLKVRANLVVPMVIDDQLFGLLIAHQCSEPRQWQEIEIDQFSELASTGSLVLERLHFL 586
               SCOP domains d3vv4a_ A: automated matches                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee.....hhhhh........hhhhhhhhh...eee.hhhhh..hhhhhhhhhhhh..eeeeeeeee..eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vv4 A   6 LSELRDRQAIFETLVAKGRELLACDRVIVYAFDDNYVGTVVAESVAEGWPQARDQVIEDPCFREHWVEAYRQGRIQATTDIFKAGLTECHLNQLRPLKVRANLVVPMVIDDQLFGLLIAHQCSEPRQWQEIEIDQFSELASTGSLVLERLHFL 158
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155   


Chain B from PDB  Type:PROTEIN  Length:160
 aligned with Q8DLC7_THEEB | Q8DLC7 from UniProtKB/TrEMBL  Length:940

    Alignment length:162
                                   434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584  
         Q8DLC7_THEEB   425 DCLRQAAVQLSELRDRQAIFETLVAKGRELLACDRVIVYAFDDNYVGTVVAESVAEGWPQARDQVIEDPCFREHWVEAYRQGRIQATTDIFKAGLTECHLNQLRPLKVRANLVVPMVIDDQLFGLLIAHQCSEPRQWQEIEIDQFSELASTGSLVLERLHFL 586
               SCOP domains d3v  v4b_ B: automated matches                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...--...hhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee.....hhhhh.........hhhhhhhh...eee.hhhhh..hhhhhhhhhhhh..eeeeeeeee..eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vv4 B  -1 DHM--AAVQLSELRDRQAIFETLVAKGRELLACDRVIVYAFDDNYVGTVVAESVAEGWPQARDQVIEDPCFREHWVEAYRQGRIQATTDIFKAGLTECHLNQLRPLKVRANLVVPMVIDDQLFGLLIAHQCSEPRQWQEIEIDQFSELASTGSLVLERLHFL 158
                              |  |   6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156  
                              1  2
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VV4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VV4)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8DLC7_THEEB | Q8DLC7)
molecular function
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
    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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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        Q8DLC7_THEEB | Q8DLC7: 2m7u 2m7v 4fof 4glq

(-) Related Entries Specified in the PDB File

3w2z