PDBsum entry 1eqd

Signaling protein

PDB id: 1eqd

Contents

Protein chain

184 a.a. *

Ligands

CYN-HEV

CIT

Waters ×200

* Residue conservation analysis

PDB id:

1eqd

Name:

Signaling protein

Title:

Crystal structure of nitrophorin 4 complexed with cn

Structure:

Nitrophorin 4. Chain: a

Source:

Rhodnius prolixus. Organism_taxid: 13249. Other_details: saliva

Biol. unit:

Dimer (from PQS)

Resolution:

1.60Å R-factor: 0.200 R-free: 0.260

Authors:

A.Weichsel,J.F.Andersen,S.A.Roberts,W.R.Montfort

Key ref:

A.Weichsel et al. (2000). Nitric oxide binding to nitrophorin 4 induces complete distal pocket burial. Nat Struct Biol, 7, 551-554. PubMed id: 10876239 DOI: 10.1038/76769

Date:

03-Apr-00 Release date: 03-May-00

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 = HEV) matches with 91.30% similarity)

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

reference

DOI no: 10.1038/76769

Nat Struct Biol 7:551-554 (2000)

PubMed id: 10876239

Nitric oxide binding to nitrophorin 4 induces complete distal pocket burial.

A.Weichsel, J.F.Andersen, S.A.Roberts, W.R.Montfort.

ABSTRACT

The nitrophorins comprise an unusual family of proteins that use ferric (Fe(III)) heme to transport highly reactive nitric oxide (NO) from the salivary gland of a blood sucking bug to the victim, resulting in vasodilation and reduced blood coagulation. We have determined structures of nitrophorin 4 in complexes with H2O, cyanide and nitric oxide. These structures reveal a remarkable feature: the nitrophorins have a broadly open distal pocket in the absence of NO, but upon NO binding, three or more water molecules are expelled and two loops fold into the distal pocket, resulting in the packing of hydrophobic groups around the NO molecule and increased distortion of the heme. In this way, the protein apparently forms a 'hydrophobic trap' for the NO molecule. The structures are very accurate, ranging between 1.6 and 1.4 A resolutions.

Selected figure(s)

Figure 3.
Figure 3. Loop ordering on NO binding. Space filling views of the distal pockets in the NP4 -NO (left) and NP4 -CN- (right) structures. The view is from above the distal pocket, with heme shown in black, heme oxygens in orange, NO in magenta, CN- in cyan, five water molecules in red, and loops A-B and G-H in green. Binding of NO leads to reordering of the A-B and G-H loops, expulsion of the water molecules, burying of NO and Asp 30, and packing of Leu 130 against the NO molecule.

Figure 4.
Figure 4. Hydrogen bonding in the mobile loops. a, Stereo view of the distal pocket in NP4 -NO. b, Stereo view of the N-terminus in NP4 -NO. c, Stereo view of the closed (red lines) and open (green lines) conformers of NP4, after superimposing them. In (a) and (b), bonds are open for Asp 30 and filled for the other residues. Nitrogens are indicated by large open spheres, carbons by small open spheres, oxygens by shaded spheres, and hydrogen bonds by dashed lines.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 551-554) copyright 2000.

Figures were selected by the author.