3TGC

Crystal structure of L130R mutant of Nitrophorin 4 from Rhodnius prolixus complexed with nitrite at pH 7.4

Summary for 3TGC

• Entry DOI: 10.2210/pdb3tgc/pdb
• Related: 3TGA 3TGB
• Descriptor: Nitrophorin-4, PROTOPORPHYRIN IX CONTAINING FE, NITRITE ION, ... (4 entities in total)
• Functional Keywords: heme, lipocalin, nitrophorin, metal binding protein
• Biological source: Rhodnius prolixus (Triatomid bug)
• Cellular location: Secreted: Q94734
• Total number of polymer chains: 1
• Total formula weight: 20999.19

Authors

Ogata, H.,He, C.,Knipp, M. (deposition date: 2011-08-17, release date: 2012-08-22, Last modification date: 2024-10-16)

Primary citation

He, C.,Ogata, H.,Knipp, M.
Insertion of an H-Bonding Residue into the Distal Pocket of the Ferriheme Protein Nitrophorin 4: Effect on Nitrite[BOND]Iron Coordination and Nitrite Disproportionation
Chem.Biodivers., 9:1761-1775, 2012

PubMed Abstract: Heme proteins are important entities for the metabolism of nitrite. Inspection of the structural features of the reported hemoprotein-nitrite crystal structures reveals that, except for nitrophorin 4 (NP4), H-bonding to the nitrite ligand is accomplished via histidine or arginine residues. These H-bonds probably play an important role for the nitrite coordination and/or reactivities. In nitrophorins, which catalyze the nitrite disproportionation reaction, such a residue is missing. Here, we report on the L130R mutant of the NP isoprotein NP4 that provides the Arg130 residue as part of the flexible G-H loop as a potential H-bonding residue in the distal heme pocket. Similar to the wild-type protein, nitrite remains N-bonded in the crystal structure of NP4(L130R). However, spectroscopic investigations show that, in solution, a second ligand-rotational orientation exists, which is in fast-exchange equilibrium with the normal, parallel ligand orientation. Moreover, the nitrite disproportionation is inhibited in NP4(L130R). Comparison with another, also less active mutant NP4(D30N) suggests that the displacement of H(2)O molecules from the heme cavity prevents the proton donation pathway through Asp30.

PubMed: 22976968
DOI: 10.1002/cbdv.201100401

Experimental method

X-RAY DIFFRACTION (1.4 Å)