3ZOX

Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (monoclinic space group)

Summary for 3ZOX

• Entry DOI: 10.2210/pdb3zox/pdb
• Related: 3ZOW 3ZOY 4JCG
• Descriptor: CYTOCHROME C-552, HEME C (3 entities in total)
• Functional Keywords: hemeprotein, electron transport
• Biological source: NITROSOMONAS EUROPAEA
• Cellular location: Periplasm: P95339
• Total number of polymer chains: 4
• Total formula weight: 35984.41

Authors

Hersleth, H.-P.,Can, M.,Krucinska, J.,Zoppellaro, G.,Andersen, N.H.,Wedekind, J.E.,Andersson, K.K.,Bren, K.L. (deposition date: 2013-02-26, release date: 2013-08-14, Last modification date: 2023-12-20)

Primary citation

Can, M.,Krucinska, J.,Zoppellaro, G.,Andersen, N.H.,Wedekind, J.E.,Hersleth, H.-P.,Andersson, K.K.,Bren, K.L.
Structural Characterization of Nitrosomonas Europaea Cytochrome C-552 Variants with Marked Differences in Electronic Structure.
Chembiochem, 14:1828-, 2013

PubMed Abstract: Nitrosomonas europaea cytochrome c-552 (Ne c-552) variants with the same His/Met axial ligand set but with different EPR spectra have been characterized structurally, to aid understanding of how molecular structure determines heme electronic structure. Visible light absorption, Raman, and resonance Raman spectroscopy of the protein crystals was performed along with structure determination. The structures solved are those of Ne c-552, which displays a "HALS" (or highly anisotropic low-spin) EPR spectrum, and of the deletion mutant Ne N64Δ, which has a rhombic EPR spectrum. Two X-ray crystal structures of wild-type Ne c-552 are reported; one is of the protein isolated from N. europaea cells (Ne c-552n, 2.35 Å resolution), and the other is of recombinant protein expressed in Escherichia coli (Ne c-552r, 1.63 Å resolution). Ne N64Δ crystallized in two different space groups, and two structures are reported [monoclinic (2.1 Å resolution) and hexagonal (2.3 Å resolution)]. Comparison of the structures of the wild-type and mutant proteins reveals that heme ruffling is increased in the mutant; increased ruffling is predicted to yield a more rhombic EPR spectrum. The 2.35 Å Ne c-552n structure shows 18 molecules in the asymmetric unit; analysis of the structure is consistent with population of more than one axial Met configuration, as seen previously by NMR. Finally, the mutation was shown to yield a more hydrophobic heme pocket and to expel water molecules from near the axial Met. These structures reveal that heme pocket residue 64 plays multiple roles in regulating the axial ligand orientation and the interaction of water with the heme. These results support the hypothesis that more ruffled hemes lead to more rhombic EPR signals in cytochromes c with His/Met axial ligation.

PubMed: 23908017
DOI: 10.1002/CBIC.201300118

Experimental method

X-RAY DIFFRACTION (2.1 Å)