PDBsum entry 1x8o

Ligand binding protein

PDB id: 1x8o

Contents

Protein chain

184 a.a. *

Ligands

PO4

HEM-_NO

Waters ×395

* Residue conservation analysis

PDB id:

1x8o

Name:

Ligand binding protein

Title:

1.01 a crystal structure of nitrophorin 4 from rhodnius prolixus complexed with nitric oxide at ph 5.6

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:

1.01Å R-factor: 0.103 R-free: 0.130

Authors:

D.A.Kondrashov,S.A.Roberts,A.Weichsel,W.R.Montfort

Key ref:

D.A.Kondrashov et al. (2004). Protein functional cycle viewed at atomic resolution: conformational change and mobility in nitrophorin 4 as a function of pH and NO binding. Biochemistry, 43, 13637-13647. PubMed id: 15504026 DOI: 10.1021/bi0483155

Date:

18-Aug-04 Release date: 05-Oct-04

Protein chain

Q94734  (NP4_RHOPR) -  Nitrophorin-4 from Rhodnius prolixus

Seq: 205 a.a.

Struc: 185 a.a.

Enzyme reactions

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

3 × nitrite + 2 × H(+) = 2 × nitric oxide + nitrate + H2O (Bound ligand (Het Group name = NO) corresponds exactly)

• 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/bi0483155

Biochemistry 43:13637-13647 (2004)

PubMed id: 15504026

Protein functional cycle viewed at atomic resolution: conformational change and mobility in nitrophorin 4 as a function of pH and NO binding.

D.A.Kondrashov, S.A.Roberts, A.Weichsel, W.R.Montfort.

ABSTRACT

The blood-sucking insect Rhodnius prolixus uses nitrophorin 4, a heme protein, to deliver nitric oxide (NO) to a victim, causing vasodilation and improved feeding. Binding of NO occurs at a ferric heme and is modulated by pH. NO binding at lower pH induces a large conformational change involving loops A-B and G-H that leads to distal pocket desolvation and protection of the nitrosyl heme complex. We have determined the crystal structures of Rhodnius nitrophorin 4 to ultrahigh resolution in four functional states: +/-NO at pH = 7.4 and +/-NO at pH = 5.6. The structure with NO at pH 7.4 (1.08 A) is newly determined while the other complexes have been modeled to resolutions much greater than previously reported (1.0-0.85 A). The ultrahigh resolution allowed us to resolve multiple conformers in binding-site loops, leading to a detailed description of the dynamics involved with storing NO in the insect salivary gland at low pH, and releasing NO in response to the increased pH of a victim's tissue. Strikingly, features for both the "open" and "closed" conformers exist under all conditions, suggesting that the flexible loops can transition with relative ease between conformational states. Yet, release of NO from rNP4 is much slower than found for other ferric heme proteins. The structures suggest that highly mobile loops can limit diffusion of diatomic molecules into and out of a protein cavity, a result with implications for the role of protein dynamics in function.