4HVK

Crystal structure and functional studies of an unusual L-cysteine desulfurase from Archaeoglobus fulgidus.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.108 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure and functional studies of an unusual L-cysteine desulfurase from Archaeoglobus fulgidus.

Yamanaka, Y.Zeppieri, L.Nicolet, Y.Marinoni, E.N.de Oliveira, J.S.Odaka, M.Dean, D.R.Fontecilla-Camps, J.C.

(2013) Dalton Trans 42: 3092-3099

  • DOI: 10.1039/c2dt32101g

  • PubMed Abstract: 
  • L-Cysteine desulfurase IscS and scaffold IscU proteins are universally involved in Fe/S cluster synthesis. The Archaeoglobus fulgidus (Af) genome encodes proteins having a high degree of primary structure similarity to IscS and IscU from other organi ...

    L-Cysteine desulfurase IscS and scaffold IscU proteins are universally involved in Fe/S cluster synthesis. The Archaeoglobus fulgidus (Af) genome encodes proteins having a high degree of primary structure similarity to IscS and IscU from other organisms. However, AfIscS is unusual because it lacks the active site lysine residue that normally forms an internal Schiff base with pyridoxal-phosphate (PLP) and serves as a base during catalysis. Our as-isolated recombinant AfIscS contains pyridoxamine phosphate (PMP) instead of the expected PLP and lacks desulfurase activity. We have solved its structure to 1.43 Å resolution and found that PMP binds non-covalently at the PLP site of the enzyme and displays significant disorder. However, the previously reported structure of recombinant Af(IscU-D35A-IscS)(2) contains an in vivo generated [Fe(2)S(2)] species within AfIscU and the question arises as to how its sulfides were generated. Here, we report that adding PLP to AfIscS produces an enzyme that displays in vitro L-cysteine desulfurase activity mediating the synthesis of a stable holo Af(IscU-D35A-IscS) complex.


    Organizational Affiliation

    Department of Biotechnology and Life Science Graduate School of Technology, Tokyo University of Agriculture and Technology, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable cysteine desulfurase 2
A
382Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)Mutation(s): 0 
Gene Names: iscS2
EC: 2.8.1.7
Find proteins for O29689 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O29689
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PMP
Query on PMP

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Download CCD File 
A
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
PYRIDOXAMINE-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.108 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 70.060α = 90.00
b = 99.270β = 90.00
c = 108.860γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
ADSCdata collection
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2013-04-24
    Type: Database references