390424

Protein Summary

This is a protein of unknown function and part of JCSG's "MG" mega-family target list (cystatin-like fold, SCOP id 54402). Cystatins are cysteine protease inhibitors (Ref 1, Ref2, Ref3) and there are several kinds of cystatins. They usually contain cysteines which may or may not be involved in intramolecular disulfide bond formation.

This target does not contain any cysteine residues. It is characterized by alpha helices surrounded by an antiparallel beta sheet.

PSI-BLAST shows hits to many proteins of unknown function/conserved hypothetical proteins from numerous bacteria. There are also significant hits to isomerases. There are no structures of proteins that are close in sequence.

This protein shares sequence similarity with the SnoaL-like polyketide cyclase (PF07366) family from PfamA (E-value: 0.0074), which is part of the NTF2 (CL0051) clan, and the PB025944 family from PfamB (E-value: 4.0e-62).

There are 2 protomers in the asymmetric unit of the unit cell in the crystal. Crystal packing analysis suggests that the oligomeric state in solution should be a monomer (Fig 1):

A search for structurally similar proteins using SSM results in significant hits (Q-score > 0.5, Z-score > 5.0) with several proteins with PDB ids (Fig 2): 2rgq (red, Crystal structure of domain of unknown function with a cystatin-like fold (ZP_00111510.1) from Nostoc punctiforme PCC 73102, JCSG structure); 1isk (yellow,  3-oxo-delta5-steroid isomerase); 1w02 (grey, ketosteroid isomerase from P. putida biotype B); 1gy7 (green, S. cerevisiae NTF2); and 1of5 (orange, MEX67-MTR2). 

Of the 4 amino acids implicated in catalysis in the ketosteroid isomerase (Y16, Y32, Y57, D103; PDB 1w02, Ref 4), there are two residues conserved in this target Tyr11 and Trp31 (Fig 3):

This coud therefore be the putative active site and this could be an isomerase or isomerase-like protein with cystatin-like fold.

References:

1)  Bode W, Engh R, Musil D, Thiele U, Huber R, Karshikov A, Brzin J, Kos J, Turk V. The 2.0 A X-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteinases. EMBO J. 1988 Aug;7(8):2593-9.

2) Stubbs MT, Laber B, Bode W, Huber R, Jerala R, Lenarcic B, Turk V. The refined 2.4 A X-ray crystal structure of recombinant human stefin B in complex with the cysteine proteinase papain: a novel type of proteinase inhibitor interaction. EMBO J. 1990 Jun;9(6):1939-47.

3) Jenko S, Dolenc I, Guncar G, Dobersek A, Podobnik M, Turk D. Crystal structure of Stefin A in complex with cathepsin H: N-terminal residues of inhibitors can adapt to the active sites of endo- and exopeptidases.
J Mol Biol. 2003 Feb 21;326(3):875-85.

4) Jang DS, Cha HJ, Cha SS, Hong BH, Ha NC, Lee JY, Oh BH, Lee HS, Choi KY.  (2004) Structural double-mutant cycle analysis of a hydrogen bond network in ketosteroid isomerase from Pseudomonas putida biotype B. Biochem.J. 382:967-973

Ligand Summary