PDBsum entry 1ywc

Ligand binding protein, blood clotting

PDB id: 1ywc

Contents

Protein chain

184 a.a. *

Ligands

HEM-CMO

Waters ×348

* Residue conservation analysis

PDB id:

1ywc

Name:

Ligand binding protein, blood clotting

Title:

Structure of the ferrous co complex of np4 from rhodnius prolixus at ph 7.0

Structure:

Nitrophorin 4. Chain: a. Synonym: np4. Engineered: yes

Source:

Rhodnius prolixus. Organism_taxid: 13249. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.00Å R-factor: 0.121 R-free: 0.150

Authors:

E.M.Maes,A.Weichsel,S.A.Roberts,W.R.Montfort

Key ref:

E.M.Maes et al. (2005). Ultrahigh resolution structures of nitrophorin 4: heme distortion in ferrous CO and NO complexes. Biochemistry, 44, 12690-12699. PubMed id: 16171383 DOI: 10.1021/bi0506573

Date:

17-Feb-05 Release date: 04-Oct-05

Protein chain

Q94734  (NP4_RHOPR) -  Nitrophorin-4 from Rhodnius prolixus

Seq: 205 a.a.

Struc: 184 a.a.

Enzyme reactions

• Enzyme class: E.C.1.7.6.1 - nitrite dismutase.
• Reaction: 3 nitrite + 2 H⁺ = 2 nitric oxide + nitrate + H2O
• Cofactor: Heme b

Heme b (Bound ligand (Het Group name = HEM) matches with 95.45% similarity)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi0506573

Biochemistry 44:12690-12699 (2005)

PubMed id: 16171383

Ultrahigh resolution structures of nitrophorin 4: heme distortion in ferrous CO and NO complexes.

E.M.Maes, S.A.Roberts, A.Weichsel, W.R.Montfort.

ABSTRACT

Nitrophorin 4 (NP4), a nitric oxide (NO)-transport protein from the blood-sucking insect Rhodnius prolixus, uses a ferric (Fe3+) heme to deliver NO to its victims. NO binding to NP4 induces a large conformational change and complete desolvation of the distal pocket. The heme is markedly nonplanar, displaying a ruffling distortion postulated to contribute to stabilization of the ferric iron. Here, we report the ferrous (Fe2+) complexes of NP4 with NO, CO, and H2O formed after chemical reduction of the protein and the characterization of these complexes by absorption spectroscopy, flash photolysis, and ultrahigh-resolution crystallography (resolutions vary from 0.9 to 1.08 A). The absorption spectra, both in solution and in the crystal, are typical for six-coordinated ferrous complexes. Closure and desolvation of the distal pocket occurs upon binding CO or NO to the iron regardless of the heme oxidation state, confirming that the conformational change is driven by distal ligand polarity. The degree of heme ruffling is coupled to the nature of the ligand and the iron oxidation state in the following order: (Fe3+)-NO > (Fe2+)-NO > (Fe2+)-CO > (Fe3+)-H2O > (Fe2+)-H2O. The ferrous coordination geometry is as expected, except for the proximal histidine bond, which is shorter than typically found in model compounds. These data are consistent with heme ruffling and coordination geometry serving to stabilize the ferric state of the nitrophorins, a requirement for their physiological function. Possible roles for heme distortion and NO bending in heme protein function are discussed.