7YR9

Crystal structure of the immature form of TtPetA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 

wwPDB Validation   3D Report Full Report


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Literature

Structure of a putative immature form of a Rieske-type iron-sulfur protein in complex with zinc chloride.

Tsutsumi, E.Niwa, S.Takeda, R.Sakamoto, N.Okatsu, K.Fukai, S.Ago, H.Nagao, S.Sekiguchi, H.Takeda, K.

(2023) Commun Chem 6: 190-190

  • DOI: https://doi.org/10.1038/s42004-023-01000-6
  • Primary Citation of Related Structures:  
    7YR9, 7YRA

  • PubMed Abstract: 

    Iron-sulfur clusters are prosthetic groups of proteins involved in various biological processes. However, details of the immature state of the iron-sulfur cluster into proteins have not yet been elucidated. We report here the first structural analysis of the Zn-containing form of a Rieske-type iron-sulfur protein, PetA, from Thermochromatium tepidum (TtPetA) by X-ray crystallography and small-angle X-ray scattering analysis. The Zn-containing form of TtPetA was indicated to be a dimer in solution. The zinc ion adopts a regular tetra-coordination with two chloride ions and two cysteine residues. Only a histidine residue in the cluster-binding site exhibited a conformational difference from the [2Fe-2S] containing form. The Zn-containing structure indicates that the conformation of the cluster binding site is already constructed and stabilized before insertion of [2Fe-2S]. The binding mode of ZnCl 2 , similar to the [2Fe-2S] cluster, suggests that the zinc ions might be involved in the insertion of the [2Fe-2S] cluster.


  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase iron-sulfur subunit
A, B
149Thermochromatium tepidumMutation(s): 0 
Gene Names: petA
EC: 7.1.1.8
UniProt
Find proteins for D1MZ11 (Thermochromatium tepidum)
Explore D1MZ11 
Go to UniProtKB:  D1MZ11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD1MZ11
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
L [auth B]
M [auth B]
N [auth B]
F [auth A],
G [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
J [auth B],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.596α = 90
b = 98.711β = 90.03
c = 51.052γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
SOLVEphasing
DMphasing
CNSrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release