2FHL

avidin related protein (AVR4)-BNA complex

Summary for 2FHL

• Entry DOI: 10.2210/pdb2fhl/pdb
• Related: 1Y52 1Y53 2FHN
• Descriptor: Avidin-related protein 4/5, 5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE, FORMIC ACID, ... (4 entities in total)
• Functional Keywords: avidin, avr4, streptavidin, high-affinity, hydrolytic activity, sugar binding protein
• Biological source: Gallus gallus (chicken)
• Cellular location: Secreted (Potential): P56734
• Total number of polymer chains: 2
• Total formula weight: 28590.05

Authors

Livnah, O.,Prizant, M. (deposition date: 2005-12-26, release date: 2006-03-21, Last modification date: 2024-10-30)

Primary citation

Prizant, M.,Eisenberg-Domovich, Y.,Hytonen, V.P.,Kulomaa, M.S.,Wilchek, M.,Bayer, E.A.,Livnah, O.
Factors dictating the pseudocatalytic efficiency of avidins
J.Mol.Biol., 358:754-763, 2006

PubMed Abstract: The hydrolysis of biotinyl p-nitrophenyl ester (BNP) by a series of avidin derivatives was examined. Surprisingly, a hyperthermostable avidin-related protein (AVR4) was shown to display extraordinary yet puzzling hydrolytic activity. In order to evaluate the molecular determinants that contribute to the reaction, the crystal structure of AVR4 was compared with those of avidin, streptavidin and key mutants of the two proteins in complex with biotinyl p-nitroanilide (BNA), the inert amide analogue of BNP. The structures revealed that a critical lysine residue contributes to the hydrolysis of BNP by avidin but has only a minor contribution to the AVR4-mediated reaction. Indeed, the respective rates of hydrolysis among the different avidins reflect several molecular parameters, including binding-site architecture, the availability of the ligand to solvent and the conformation of the ligand and consequent susceptibility to efficient nucleophilic attack. In avidin, the interaction of BNP with Lys111 and disorder of the L3,4 loop (and consequent solvent availability) together comprise the major driving force behind the hydrolysis, whereas in AVR4 the status of the ligand (the pseudo-substrate) is a major distinguishing feature. In the latter protein, a unique conformation of the L3,4 loop restrains the pseudo-substrate, thereby exposing the carbonyl carbon atom to nucleophilic attack. In addition, due to its conformation, the pseudo-substrate in the AVR4 complex cannot interact with the conserved lysine analogue (Lys109); instead, this function is superseded by polar interactions with Arg112. The results demonstrate that, in highly similar proteins, different residues can perform the same function and that subtle differences in the active-site architecture of such proteins can result in alternative modes of reaction.

PubMed: 16546211
DOI: 10.1016/j.jmb.2006.02.044

Experimental method

X-RAY DIFFRACTION (1.05 Å)