1GQ1

CYTOCHROME CD1 NITRITE REDUCTASE, Y25S mutant, OXIDISED FORM

Summary for 1GQ1

• Entry DOI: 10.2210/pdb1gq1/pdb
• Related: 1H9X 1H9Y 1HCM 1HJ3 1HJ4 1HJ5
• Descriptor: CYTOCHROME CD1 NITRITE REDUCTASE, HEME C, HEME D, ... (6 entities in total)
• Functional Keywords: reductase, enzyme, nitrite reductase, oxidoreductase, denitrification, electron transport, periplasmic
• Biological source: PARACOCCUS PANTOTROPHUS
• Total number of polymer chains: 2
• Total formula weight: 128647.64

Authors

Sjogren, T.,Gordon, E.H.J.,Lofqvist, M.,Richter, C.D.,Hajdu, J.,Ferguson, S.J. (deposition date: 2001-11-19, release date: 2002-11-28, Last modification date: 2024-10-23)

Primary citation

Gordon, E.H.J.,Sjogren, T.,Lofqvist, M.,Richter, C.D.,Allen, J.,Higham, C.,Hajdu, J.,Fulop, V.,Ferguson, S.J.
Structure and Kinetic Properties of Paracoccus Pantotrophus Cytochrome Cd1 Nitrite Reductase with the D1 Heme Active Site Ligand Tyrosine 25 Replaced by Serine
J.Biol.Chem., 278:11773-, 2003

PubMed Abstract: The 1.4-A crystal structure of the oxidized state of a Y25S variant of cytochrome cd(1) nitrite reductase from Paracoccus pantotrophus is described. It shows that loss of Tyr(25), a ligand via its hydroxy group to the iron of the d(1) heme in the oxidized (as prepared) wild-type enzyme, does not result in a switch at the c heme of the unusual bishistidinyl coordination to the histidine/methionine coordination seen in other conformations of the enzyme. The Ser(25) side chain is seen in two positions in the d(1) heme pocket with relative occupancies of approximately 7:3, but in neither case is the hydroxy group bound to the iron atom; instead, a sulfate ion from the crystallization solution is bound between the Ser(25) side chain and the heme iron. Unlike the wild-type enzyme, the Y25S mutant is active as a reductase toward nitrite, oxygen, and hydroxylamine without a reductive activation step. It is concluded that Tyr(25) is not essential for catalysis of reduction of any substrate, but that the requirement for activation by reduction of the wild-type enzyme is related to a requirement to drive the dissociation of this residue from the active site. The Y25S protein retains the d(1) heme less well than the wild-type protein, suggesting that the tyrosine residue has a role in stabilizing the binding of this cofactor.

PubMed: 12556530
DOI: 10.1074/JBC.M211886200

Experimental method

X-RAY DIFFRACTION (1.4 Å)