Protein Science, Vol 9, Issue 12 2329-2337, Copyright © 2000 by Cold Spring Harbor Laboratory Press

JOURNAL ARTICLE

Structural comparison of Ntn-hydrolases

C Oinonen and J Rouvinen
Department of Chemistry, University of Joensuu, Finland. Carita.Oinonen@joensuu.fi

The Ntn-hydrolases (N-terminal nucleophile) are a superfamily of diverse enzymes that has recently been characterized. All of the proteins in this family are activated autocatalytically; they contain an N-terminally located catalytic nucleophile, and they cleave an amide bond. In the present study, the structures of four enzymes of this superfamily are compared in more detail. Although the amino acid sequence homology is almost completely absent, the enzymes share a similar alphabeta betaalpha-core structure. The central beta-sheets in the core were found to have different packing angles, ranging from 5 to 35 degrees. In the Ntn-hydrolases under study, eight totally conserved secondary structure units were found (region C). Five of them were observed to contain the greatest number of conserved and functionally important residues and are therefore crucial for the structure and function of Ntn-hydrolases. Two additional regions, consisting of secondary structure units (regions A and B), were found to be in structurally similar locations, but in different orders in the polypeptide chain. The catalytic machinery is located in the structures in a similar manner, and thus the catalytic mechanisms of all of the enzymes are probably similar. However, the substrate binding and the oxyanion hole differed partially.
CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

This article has been cited by other articles:

				O. D. Ekici, M. Paetzel, and R. E. Dalbey Unconventional serine proteases: Variations on the catalytic Ser/His/Asp triad configuration Protein Sci., December 1, 2008; 17(12): 2023 - 2037. [Abstract] [Full Text] [PDF]

				K. Michalska, A. Hernandez-Santoyo, and M. Jaskolski The Mechanism of Autocatalytic Activation of Plant-type L-Asparaginases J. Biol. Chem., May 9, 2008; 283(19): 13388 - 13397. [Abstract] [Full Text] [PDF]

				Y. Sun and H.-C. Guo Structural constraints on autoprocessing of the human nucleoporin Nup98 Protein Sci., March 1, 2008; 17(3): 494 - 505. [Abstract] [Full Text] [PDF]

				J. Carey, S. Lindman, M. Bauer, and S. Linse Protein reconstitution and three-dimensional domain swapping: Benefits and constraints of covalency Protein Sci., November 1, 2007; 16(11): 2317 - 2333. [Abstract] [Full Text] [PDF]

				G. Boanca, A. Sand, T. Okada, H. Suzuki, H. Kumagai, K. Fukuyama, and J. J. Barycki Autoprocessing of Helicobacter pylori {gamma}-Glutamyltranspeptidase Leads to the Formation of a Threonine-Threonine Catalytic Dyad J. Biol. Chem., January 5, 2007; 282(1): 534 - 541. [Abstract] [Full Text] [PDF]

				R. S. Kumar, J. A. Brannigan, A. A. Prabhune, A. V. Pundle, G. G. Dodson, E. J. Dodson, and C. G. Suresh Structural and Functional Analysis of a Conjugated Bile Salt Hydrolase from Bifidobacterium longum Reveals an Evolutionary Relationship with Penicillin V Acylase J. Biol. Chem., October 27, 2006; 281(43): 32516 - 32525. [Abstract] [Full Text] [PDF]

				G. Boanca, A. Sand, and J. J. Barycki Uncoupling the Enzymatic and Autoprocessing Activities of Helicobacter pylori {gamma}-Glutamyltranspeptidase J. Biol. Chem., July 14, 2006; 281(28): 19029 - 19037. [Abstract] [Full Text] [PDF]

				B. Geueke, K. Namoto, D. Seebach, and H.-P. E. Kohler A Novel {beta}-Peptidyl Aminopeptidase (BapA) from Strain 3-2W4 Cleaves Peptide Bonds of Synthetic {beta}-Tri- and {beta}-Dipeptides J. Bacteriol., September 1, 2005; 187(17): 5910 - 5917. [Abstract] [Full Text] [PDF]

				K. Michalska, K. Brzezinski, and M. Jaskolski Crystal Structure of Isoaspartyl Aminopeptidase in Complex with L-Aspartate J. Biol. Chem., August 5, 2005; 280(31): 28484 - 28491. [Abstract] [Full Text] [PDF]

				H. Cheng and N. V. Grishin DOM-fold: A structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain Protein Sci., July 1, 2005; 14(7): 1902 - 1910. [Abstract] [Full Text] [PDF]

				G.-B. Kim, C. M. Miyamoto, E. A. Meighen, and B. H. Lee Cloning and Characterization of the Bile Salt Hydrolase Genes (bsh) from Bifidobacterium bifidum Strains Appl. Envir. Microbiol., September 1, 2004; 70(9): 5603 - 5612. [Abstract] [Full Text] [PDF]

				H. S. Kim, T. S. Kang, J. S. Hyun, and H. S. Kang Regulation of Penicillin G Acylase Gene Expression in Escherichia coli by Repressor PaaX and the cAMP-cAMP Receptor Protein Complex J. Biol. Chem., August 6, 2004; 279(32): 33253 - 33262. [Abstract] [Full Text] [PDF]

				G.-B. Kim, S.-H. Yi, and B. H. Lee Purification and Characterization of Three Different Types of Bile Salt Hydrolases from Bifidobacterium Strains J Dairy Sci, February 1, 2004; 87(2): 258 - 266. [Abstract] [Full Text] [PDF]

				J. Pei and N. V. Grishin Peptidase family U34 belongs to the superfamily of N-terminal nucleophile hydrolases Protein Sci., May 1, 2003; 12(5): 1131 - 1135. [Abstract] [Full Text] [PDF]

				Y. Wang and H.-C. Guo Two-step Dimerization for Autoproteolysis to Activate Glycosylasparaginase J. Biol. Chem., January 24, 2003; 278(5): 3210 - 3219. [Abstract] [Full Text] [PDF]