2VM3

Structure of Alcaligenes xylosoxidans in space group R3 - 1 of 2

Summary for 2VM3

• Entry DOI: 10.2210/pdb2vm3/pdb
• Related: 1BQ5 1GS6 1GS7 1GS8 1HAU 1HAW 1NDT 1OE1 1OE2 1OE3 1WA0 1WA1 1WA2 1WAE 2BO0 2BP0 2BP8 2JFC 2VM4
• Descriptor: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE, COPPER (II) ION, ZINC ION, ... (5 entities in total)
• Functional Keywords: denitrification, nitrite reductase, ordered mechanism, oxidoreductase
• Biological source: ACHROMOBACTER XYLOSOXIDANS
• Total number of polymer chains: 1
• Total formula weight: 36957.25

Authors

Hough, M.A.,Antonyuk, S.V.,Strange, R.W.,Eady, R.R.,Hasnain, S.S. (deposition date: 2008-01-22, release date: 2008-02-05, Last modification date: 2023-12-13)

Primary citation

Hough, M.A.,Antonyuk, S.V.,Strange, R.W.,Eady, R.R.,Hasnain, S.S.
Crystallography with Online Optical and X-Ray Absorption Spectroscopies Demonstrates an Ordered Mechanism in Copper Nitrite Reductase.
J.Mol.Biol., 378:353-, 2008

PubMed Abstract: Nitrite reductases are key enzymes that perform the first committed step in the denitrification process and reduce nitrite to nitric oxide. In copper nitrite reductases, an electron is delivered from the type 1 copper (T1Cu) centre to the type 2 copper (T2Cu) centre where catalysis occurs. Despite significant structural and mechanistic studies, it remains controversial whether the substrates, nitrite, electron and proton are utilised in an ordered or random manner. We have used crystallography, together with online X-ray absorption spectroscopy and optical spectroscopy, to show that X-rays rapidly and selectively photoreduce the T1Cu centre, but that the T2Cu centre does not photoreduce directly over a typical crystallographic data collection time. Furthermore, internal electron transfer between the T1Cu and T2Cu centres does not occur, and the T2Cu centre remains oxidised. These data unambiguously demonstrate an 'ordered' mechanism in which electron transfer is gated by binding of nitrite to the T2Cu. Furthermore, the use of online multiple spectroscopic techniques shows their value in assessing radiation-induced redox changes at different metal sites and demonstrates the importance of ensuring the correct status of redox centres in a crystal structure determination. Here, optical spectroscopy has shown a very high sensitivity for detecting the change in T1Cu redox state, while X-ray absorption spectroscopy has reported on the redox status of the T2Cu site, as this centre has no detectable optical absorption.

PubMed: 18353369
DOI: 10.1016/J.JMB.2008.01.097

Experimental method

X-RAY DIFFRACTION (1.8 Å)