2OF9

Crystal structure of apo AVR4 (D39A/C122S)

Summary for 2OF9

• Entry DOI: 10.2210/pdb2of9/pdb
• Related: 1Y53 2FHL 2OF8 2OFA 2OFB
• Descriptor: Avidin-related protein 4/5, FORMIC ACID (3 entities in total)
• Functional Keywords: avidin, streptavidin, avr4, high affinity, pseudo catalysis, ligand binding protein
• Biological source: Gallus gallus (chicken)
• Cellular location: Secreted (Potential): P56734
• Total number of polymer chains: 2
• Total formula weight: 28920.24

Authors

Livnah, O.,Hayouka, R.,Eisenberg-Domovich, Y. (deposition date: 2007-01-03, release date: 2007-12-25, Last modification date: 2024-10-16)

Primary citation

Hayouka, R.,Eisenberg-Domovich, Y.,Hytonen, V.P.,Maatta, J.A.,Nordlund, H.R.,Kulomaa, M.S.,Wilchek, M.,Bayer, E.A.,Livnah, O.
Critical importance of loop conformation to avidin-enhanced hydrolysis of an active biotin ester.
Acta Crystallogr.,Sect.D, 64:302-308, 2008

PubMed Abstract: The homotetrameric and biotin-binding properties of avidin and streptavidin have been exploited for a myriad of biotechnological applications and theoretical studies. Among the few differences between the two proteins is the capacity of avidin to hydrolyze biotinyl p-nitrophenyl ester (BNP), as opposed to streptavidin, which fully protects the same pseudosubstrate from hydrolysis. Combined mutagenesis and X-ray analysis have been used to attempt to understand this diametric difference in activities. It was found that a charged residue and one of the loops (L3,4) are together responsible for this difference. Recently, the avidin-related analogue AVR4 was found to have an even more pronounced BNP-hydrolysis activity than avidin. Again, the combination of charged residue(s) (Asp39 and/or Arg112) and the rigid conformation of the L3,4 loop was suggested to be responsible for the observed hydrolysis reaction. However, replacement of the latter charged residues in AVR4 resulted in only a modest reduction in hydrolytic activity at most, whereas replacement of the L3,4 loop of avidin with the rigid loop of AVR4 caused a dramatic increase in the activity of avidin. These results clearly demonstrate that the main feature responsible for the observed differences in rates of hydrolysis among the avidins is the conformational status of the L3,4 loop, which imposes conformational constraints on the pseudosubstrate, thereby rendering it susceptible to nucleophilic attack by solvent. In this context, the hydrolytic properties of the avidins reflect enzyme catalysis, in that subtleties in substrate binding are the determining features of catalytic efficiency.

PubMed: 18323625
DOI: 10.1107/S0907444907067844

Experimental method

X-RAY DIFFRACTION (1.35 Å)