2VMJ

Type 1 Copper-Binding Loop of Nitrite Reductase mutant: 130- CAPEGMVPWHVVSGM-144 to 130-CTPHPFM-136

Summary for 2VMJ

• Entry DOI: 10.2210/pdb2vmj/pdb
• Related: 1BQ5 1GS6 1GS7 1GS8 1HAU 1HAW 1NDT 1OE1 1OE2 1OE3 1WA0 1WA1 1WA2 1WAE 2BO0 2BP0 2BP8 2JFC 2VM3 2VM4
• Descriptor: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE, ZINC ION, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... (4 entities in total)
• Functional Keywords: cupredoxin, type 1 copper, type 2 copper, electron transfer, loop-directed mutagenesis, copper-containing nitrite reductase, oxidoreductase
• Biological source: ALCALIGENES XYLOSOXYDANS XYLOSOXYDANS
• Total number of polymer chains: 1
• Total formula weight: 36368.37

Authors

Sato, K.,Firbank, S.J.,Li, C.,Banfield, M.J.,Dennison, C. (deposition date: 2008-01-28, release date: 2008-12-23, Last modification date: 2023-12-13)

Primary citation

Sato, K.,Firbank, S.J.,Li, C.,Banfield, M.J.,Dennison, C.
The Importance of the Long Type 1 Copper-Binding Loop of Nitrite Reductase for Structure and Function.
Chemistry, 14:5820-, 2008

PubMed Abstract: The long 15-residue type 1 copper-binding loop of nitrite reductase has been replaced with that from the cupredoxin amicyanin (7 residues). This sizable loop contraction does not have a significant effect on the spectroscopy, and therefore, the structures of both the type 1 and type 2 Cu(II) sites. The crystal structure of this variant with Zn(II) at both the type 1 and type 2 sites has been determined. The coordination geometry of the type 2 site is almost identical to that found in the wild-type protein. However, the structure of the type 1 centre changes significantly upon metal substitution, which is an unusual feature for this class of site. The positions of most of the coordinating residues are altered of which the largest difference was observed for the coordinating His residue in the centre of the mutated loop. This ligand moves away from the active site, which results in a more open metal centre with a coordinating water molecule. Flexibility has been introduced into this region of the protein. The 200 mV increase in the reduction potential of the type 1 copper site indicates that structural changes upon reduction must stabilise the cuprous form. The resulting unfavourable driving force for electron transfer between the two copper sites, and an increased reorganisation energy for the type 1 centre, contribute to the loop variant having very little nitrite reductase activity. The extended type 1 copper-binding loop of this enzyme makes a number of interactions that are important for maintaining quaternary structure.

PubMed: 18491346
DOI: 10.1002/CHEM.200701997

Experimental method

X-RAY DIFFRACTION (2.5 Å)