5B87

Crystal structure of a Cysteine Desulfurase from Thermococcus onnurineus NA1 in complex with alanine at 2.3 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Catalytic Intermediate Crystal Structures of Cysteine Desulfurase from the ArchaeonThermococcus onnurineus NA1.

Ho, T.-H.Huynh, K.-H.Nguyen, D.Q.Park, H.Jung, K.Sur, B.Ahn, Y.-J.Cha, S.-S.Kang, L.-W.

(2017) Archaea 2017: 5395293-5395293

  • DOI: 10.1155/2017/5395293
  • Primary Citation of Related Structures:  
    5B7S, 5B7U, 5B87, 5B89

  • PubMed Abstract: 
  • Thermococcus onnurineus NA1 is an anaerobic archaeon usually found in a deep-sea hydrothermal vent area, which can use elemental sulfur (S 0 ) as a terminal electron acceptor for energy. Sulfur, essential to many biomolecules such ...

    Thermococcus onnurineus NA1 is an anaerobic archaeon usually found in a deep-sea hydrothermal vent area, which can use elemental sulfur (S 0 ) as a terminal electron acceptor for energy. Sulfur, essential to many biomolecules such as sulfur-containing amino acids and cofactors including iron-sulfur cluster, is usually mobilized from cysteine by the pyridoxal 5'-phosphate- (PLP-) dependent enzyme of cysteine desulfurase (CDS). We determined the crystal structures of CDS from Thermococcus onnurineus NA1 (ToCDS), which include native internal aldimine (NAT), gem-diamine (GD) with alanine, internal aldimine structure with existing alanine (IAA), and internal aldimine with persulfide-bound Cys356 (PSF) structures. The catalytic intermediate structures showed the dihedral angle rotation of Schiff-base linkage relative to the PLP pyridine ring. The ToCDS structures were compared with bacterial CDS structures, which will help us to understand the role and catalytic mechanism of ToCDS in the archaeon Thermococcus onnurineus NA1.


    Organizational Affiliation

    Department of Biological Sciences, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 05029, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cysteine desulfuraseAB419Thermococcus onnurineus NA1Mutation(s): 0 
Gene Names: TON_0289
EC: 2.8.1.7
Find proteins for B6YT87 (Thermococcus onnurineus (strain NA1))
Explore B6YT87 
Go to UniProtKB:  B6YT87
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
ALA
Query on ALA

Download CCD File 
A, B
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSS
Query on CSS
A,BL-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.282α = 90
b = 93.809β = 90
c = 145.534γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-06-13 
  • Released Date: 2017-06-14 
  • Deposition Author(s): Ho, T.-H., Kang, L.-W.

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2018-06-13
    Changes: Data collection, Database references