4CH7

Crystal structure of the siroheme decarboxylase NirDL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.002 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure of Siroheme Decarboxylase in Complex with Iron-Uroporphyrin III Reveals Two Essential Histidine Residues

Haufschildt, K.Schmelz, S.Kriegler, T.M.Neumann, A.Streif, J.Arai, H.Heinz, D.W.Layer, G.

(2014) J.Mol.Biol. 426: 3272

  • DOI: 10.1016/j.jmb.2014.07.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The isobacteriochlorin heme d1 serves as an essential cofactor in the cytochrome cd1 nitrite reductase NirS that plays an important role for denitrification. During the biosynthesis of heme d1, the enzyme siroheme decarboxylase catalyzes the conversi ...

    The isobacteriochlorin heme d1 serves as an essential cofactor in the cytochrome cd1 nitrite reductase NirS that plays an important role for denitrification. During the biosynthesis of heme d1, the enzyme siroheme decarboxylase catalyzes the conversion of siroheme to 12,18-didecarboxysiroheme. This enzyme was discovered recently (Bali S, Lawrence AD, Lobo SA, Saraiva LM, Golding BT, Palmer DJ et al. Molecular hijacking of siroheme for the synthesis of heme and d1 heme. Proc Natl Acad Sci USA 2011;108:18260-5) and is only scarcely characterized. Here, we present the crystal structure of the siroheme decarboxylase from Hydrogenobacter thermophilus representing the first three-dimensional structure for this type of enzyme. The overall structure strikingly resembles those of transcriptional regulators of the Lrp/AsnC family. Moreover, the structure of the enzyme in complex with a substrate analog reveals first insights into its active-site architecture. Through site-directed mutagenesis and subsequent biochemical characterization of the enzyme variants, two conserved histidine residues within the active site are identified to be involved in substrate binding and catalysis. Based on our results, we propose a potential catalytic mechanism for the enzymatic reaction catalyzed by the siroheme decarboxylase.


    Organizational Affiliation

    Institute of Organic Chemistry, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany.,Department of Biotechnology, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany.,Department of Molecular Structural Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany.,Institute of Microbiology, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany. Electronic address: g.layer@tu-braunschweig.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NIRD-LIKE PROTEIN
A
342Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6)Mutation(s): 0 
Gene Names: nirD
Find proteins for D3DFS4 (Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6))
Go to UniProtKB:  D3DFS4
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.002 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.350α = 90.00
b = 72.090β = 100.40
c = 51.200γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
AutoSolphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-08-13
    Type: Database references
  • Version 1.2: 2014-09-10
    Type: Database references