PDBsum entry 5ngx

Oxidoreductase

PDB id: 5ngx

Contents

Protein chain

126 a.a.

Ligands

HEC-NO2

GOL

Waters ×220

PDB id:

5ngx

Name:

Oxidoreductase

Title:

The 1.06 a resolution structure of the l16g mutant of ferric cytochromE C prime from alcaligenes xylosoxidans, complexed with nitrite

Structure:

Cytochrome c'. Chain: a. Engineered: yes

Source:

Alcaligenes xylosoxydans xylosoxydans. Organism_taxid: 85698. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.06Å R-factor: 0.179 R-free: 0.200

Authors:

R.Strange,M.Hough,D.Kekelli,S.Horrell,T.Moreno Chicano

Key ref:

Z.N.Nilsson et al. (2017). Distinguishing Nitro vs Nitrito Coordination in Cytochrome c' Using Vibrational Spectroscopy and Density Functional Theory. Inorg Chem, 56, 13205-13213. PubMed id: 29053273

Date:

20-Mar-17 Release date: 16-May-18

Protein chain

P00138  (CYCP_ALCXX) -  Cytochrome c' from Alcaligenes xylosoxydans xylosoxydans

Seq: 127 a.a.

Struc: 126 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Inorg Chem 56:13205-13213 (2017)

PubMed id: 29053273

Distinguishing Nitro vs Nitrito Coordination in Cytochrome c' Using Vibrational Spectroscopy and Density Functional Theory.

Z.N.Nilsson, B.L.Mandella, K.Sen, D.Kekilli, M.A.Hough, P.Moënne-Loccoz, R.W.Strange, C.R.Andrew.

ABSTRACT

Nitrite coordination to heme cofactors is a key step in the anaerobic production of the signaling molecule nitric oxide (NO). An ambidentate ligand, nitrite has the potential to coordinate via the N- (nitro) or O- (nitrito) atoms in a manner that can direct its reactivity. Distinguishing nitro vs nitrito coordination, along with the influence of the surrounding protein, is therefore of particular interest. In this study, we probed Fe(III) heme-nitrite coordination in Alcaligenes xylosoxidans cytochrome c' (AXCP), an NO carrier that excludes anions in its native state but that readily binds nitrite (K_d∼ 0.5 mM) following a distal Leu16 → Gly mutation to remove distal steric constraints. Room-temperature resonance Raman spectra (407 nm excitation) identify ν(Fe-NO₂), δ(ONO), and ν_s(NO₂) nitrite ligand vibrations in solution. Illumination with 351 nm UV light results in photoconversion to {FeNO}⁶and {FeNO}⁷states, enabling FTIR measurements to distinguish ν_s(NO₂) and ν_as(NO₂) vibrations from differential spectra. Density functional theory calculations highlight the connections between heme environment, nitrite coordination mode, and vibrational properties and confirm that nitrite binds to L16G AXCP exclusively through the N atom. Efforts to obtain the nitrite complex crystal structure were hampered by photochemistry in the X-ray beam. Although low dose crystal structures could be modeled with a mixed nitrite (nitro)/H₂O distal population, their photosensitivity and partial occupancy underscores the value of the vibrational approach. Overall, this study sheds light on steric determinants of heme-nitrite binding and provides vibrational benchmarks for future studies of heme protein nitrite reactions.