5B82

Crystal structure of the cyanobacterial heme-protein Tll0287


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

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Literature

Crystal structure and redox properties of a novel cyanobacterial heme protein with a His/Cys heme axial ligation and a Per-Arnt-Sim (PAS)-like domain

Motomura, T.Suga, M.Hienerwadel, R.Nakagawa, A.Lai, T.L.Nitschke, W.Kuma, T.Sugiura, M.Boussac, A.Shen, J.R.

(2017) J Biol Chem 292: 9599-9612

  • DOI: 10.1074/jbc.M116.746263
  • Primary Citation of Related Structures:  
    5B82

  • PubMed Abstract: 
  • Photosystem II catalyzes light-induced water oxidation leading to the generation of dioxygen indispensable for sustaining aerobic life on Earth. The Photosystem II reaction center is composed of D1 and D2 proteins encoded by psbA and psbD genes, respectively ...

    Photosystem II catalyzes light-induced water oxidation leading to the generation of dioxygen indispensable for sustaining aerobic life on Earth. The Photosystem II reaction center is composed of D1 and D2 proteins encoded by psbA and psbD genes, respectively. In cyanobacteria, different psbA genes are present in the genome. The thermophilic cyanobacterium Thermosynechococcus elongatus contains three psbA genes: psbA1 , psbA2 , and psbA3 , and a new c -type heme protein, Tll0287, was found to be expressed in a strain expressing the psbA2 gene only, but the structure and function of Tll0287 are unknown. Here we solved the crystal structure of Tll0287 at a 2.0 Å resolution. The overall structure of Tll0287 was found to be similar to some kinases and sensor proteins with a Per-Arnt-Sim-like domain rather than to other c -type cytochromes. The fifth and sixth axial ligands for the heme were Cys and His, instead of the His/Met or His/His ligand pairs observed for most of the c -type hemes. The redox potential, E ½ , of Tll0287 was -255 ± 20 mV versus normal hydrogen electrode at pH values above 7.5. Below this pH value, the E ½ increased by ≈57 mV/pH unit at 15 °C, suggesting the involvement of a protonatable group with a p K red = 7.2 ± 0.3. Possible functions of Tll0287 as a redox sensor under microaerobic conditions or a cytochrome subunit of an H 2 S-oxidizing system are discussed in view of the environmental conditions in which psbA2 is expressed, as well as phylogenetic analysis, structural, and sequence homologies.


    Organizational Affiliation

    the Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tll0287 proteinA191Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: tll0287
UniProt
Find proteins for Q8DM36 (Thermosynechococcus vestitus (strain IAM M-273 / NIES-2133 / BP-1))
Explore Q8DM36 
Go to UniProtKB:  Q8DM36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DM36
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
B [auth A]HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.246α = 90
b = 101.246β = 90
c = 33.076γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Database references