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The crystal structure of the R52Q mutant demonstrates a role for R52 in chromophore pKa regulation in photoactive yellow protein.
Biochemistry. 2006 Mar 21; 45(11):3542-7.B

Abstract

Mutating arginine 52 to glutamine (R52Q) in photoactive yellow protein (PYP) increases the pK(a) of the chromophore by 1 pH unit. The structure of the R52Q PYP mutant was determined by X-ray crystallography and was compared to the structure of wild-type PYP to assess the role of R52 in pK(a) regulation. The essential differences between R52Q and the wild type were confined to the loop region containing the 52nd residue. While the hydrogen bonds involving the chromophore were unchanged by the mutation, removing the guanidino group generated a cavity near the chromophore; this cavity is occupied by two water molecules. In the wild type, R52 forms hydrogen bonds with T50 and Y98; these hydrogen bonds are lost in R52Q. Q52 is linked to Y98 by hydrogen bonding through the two water molecules. R52 acts as a lid on the chromophore binding pocket and controls the accessibility of the exterior solvent and the pK(a) of the chromophore. R52 is found to flip out during the formation of PYP(M). The result of this movement is quite similar to the altered structure of R52Q. Thus, we propose that conformational changes at R52 are partly responsible for pK(a) regulation during the photocycle.

Authors+Show Affiliations

Structural Biology Group, Research and Utilization Division, Japan Synchrotron Radiation Research Institute, Hyogo, Japan.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Comparative Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

16533035

Citation

Shimizu, Nobutaka, et al. "The Crystal Structure of the R52Q Mutant Demonstrates a Role for R52 in Chromophore pKa Regulation in Photoactive Yellow Protein." Biochemistry, vol. 45, no. 11, 2006, pp. 3542-7.
Shimizu N, Kamikubo H, Yamazaki Y, et al. The crystal structure of the R52Q mutant demonstrates a role for R52 in chromophore pKa regulation in photoactive yellow protein. Biochemistry. 2006;45(11):3542-7.
Shimizu, N., Kamikubo, H., Yamazaki, Y., Imamoto, Y., & Kataoka, M. (2006). The crystal structure of the R52Q mutant demonstrates a role for R52 in chromophore pKa regulation in photoactive yellow protein. Biochemistry, 45(11), 3542-7.
Shimizu N, et al. The Crystal Structure of the R52Q Mutant Demonstrates a Role for R52 in Chromophore pKa Regulation in Photoactive Yellow Protein. Biochemistry. 2006 Mar 21;45(11):3542-7. PubMed PMID: 16533035.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The crystal structure of the R52Q mutant demonstrates a role for R52 in chromophore pKa regulation in photoactive yellow protein. AU - Shimizu,Nobutaka, AU - Kamikubo,Hironari, AU - Yamazaki,Yoichi, AU - Imamoto,Yasushi, AU - Kataoka,Mikio, PY - 2006/3/15/pubmed PY - 2006/5/17/medline PY - 2006/3/15/entrez SP - 3542 EP - 7 JF - Biochemistry JO - Biochemistry VL - 45 IS - 11 N2 - Mutating arginine 52 to glutamine (R52Q) in photoactive yellow protein (PYP) increases the pK(a) of the chromophore by 1 pH unit. The structure of the R52Q PYP mutant was determined by X-ray crystallography and was compared to the structure of wild-type PYP to assess the role of R52 in pK(a) regulation. The essential differences between R52Q and the wild type were confined to the loop region containing the 52nd residue. While the hydrogen bonds involving the chromophore were unchanged by the mutation, removing the guanidino group generated a cavity near the chromophore; this cavity is occupied by two water molecules. In the wild type, R52 forms hydrogen bonds with T50 and Y98; these hydrogen bonds are lost in R52Q. Q52 is linked to Y98 by hydrogen bonding through the two water molecules. R52 acts as a lid on the chromophore binding pocket and controls the accessibility of the exterior solvent and the pK(a) of the chromophore. R52 is found to flip out during the formation of PYP(M). The result of this movement is quite similar to the altered structure of R52Q. Thus, we propose that conformational changes at R52 are partly responsible for pK(a) regulation during the photocycle. SN - 0006-2960 UR - https://www.unboundmedicine.com/medline/citation/16533035/The_crystal_structure_of_the_R52Q_mutant_demonstrates_a_role_for_R52_in_chromophore_pKa_regulation_in_photoactive_yellow_protein_ L2 - https://doi.org/10.1021/bi051430a DB - PRIME DP - Unbound Medicine ER -