PDBsum entry: 1cmx

Hydrolase

PDB-id: 1cmx

Biological unit* = asymmetric unit,
as shown
(*as deduced by PQS)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

214 a.a. *

76 a.a. *

17 a.a. *

Waters ×75

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1cmx

Name:

Hydrolase

Title:

Structural basis for the specificity of ubiquitin c- terminal hydrolases

Structure:

Protein (ubiquitin yuh1-ubal). Chain: a, c. Fragment: all. Engineered: yes. Other_details: ubiquitin c-terminus modified to an aldehyde. Protein (ubiquitin yuh1-ubal). Chain: b, d. Fragment: all.

Source:

Synthetic: yes. Other_details: the protein was chemically synthesized. The sequence of this protein is naturally found in the cytoplasm of plasmid p-1a2/trpyuh1-1 of saccharomyces cerevisiae (baker's yeast). The expression system was escherichia coli, strain mm294, plasmid p-1a2/trpyuh1-1.. Escherichia coli, strain mm294, plasmid p-1a2/trpyuh1-1.

Biological unit:

Tetramer (from PQS)

UniProt:

Chains A, C: P35127 (UBL1_YEAST)

Seq:	236 a.a.
Struc:	214 a.a.

Chain B: P62988 (UBIQ_HUMAN)

Seq:	76 a.a.
Struc:	76 a.a.*

Chain D: P62988 (UBIQ_HUMAN)

Seq:

76 a.a.

Struc:

17 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 11 residue positions (black crosses)

Enzyme class:

Chains A, C: E.C.3.4.19.12   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

Resolution:

2.25Å

R-factor:

0.248

R-free:

0.285

Authors:

S.C.Johnston,S.M.Riddle,R.E.Cohen,C.P.Hill

Key ref:

S.C.Johnston et al. (1999). Structural basis for the specificity of ubiquitin C-terminal hydrolases.. EMBO J, 18, 3877-3887. [PubMed id: 10406793] [DOI: 10.1093/emboj/18.14.3877]

Date:

12-May-99

Release date:

27-Jul-99

Quick_links

Procheck

Surface

Key reference

DOI no: 10.1093/emboj/18.14.3877

EMBO J 18:3877-3887 (1999)

PubMed id: 10406793

Structural basis for the specificity of ubiquitin C-terminal hydrolases.

S.C.Johnston, S.M.Riddle, R.E.Cohen, C.P.Hill.

ABSTRACT

The release of ubiquitin from attachment to other proteins and adducts is critical for ubiquitin biosynthesis, proteasomal degradation and other cellular processes. De-ubiquitination is accomplished in part by members of the UCH (ubiquitin C-terminal hydrolase) family of enzymes. We have determined the 2.25 A resolution crystal structure of the yeast UCH, Yuh1, in a complex with the inhibitor ubiquitin aldehyde (Ubal). The structure mimics the tetrahedral intermediate in the reaction pathway and explains the very high enzyme specificity. Comparison with a related, unliganded UCH structure indicates that ubiquitin binding is coupled to rearrangements which block the active-site cleft in the absence of authentic substrate. Remarkably, a 21-residue loop that becomes ordered upon binding Ubal lies directly over the active site. Efficiently processed substrates apparently pass through this loop, and constraints on the loop conformation probably function to control UCH specificity.

Selected figure(s)

Figure 1.
Figure 1 Stereoview ribbon representation of the Yuh1–Ubal complex. (A) Ubal is not shown in this panel. Sidechains of the active-site residues Gln84, Cys90, His166 and Asp181 (red) are labeled Q, C, H and D. N- and C-termini are labeled. The disordered segment (residues 63–77) is indicated with the adjacent ordered residues labeled in magenta. The active-site-crossover loop is colored yellow. Secondary structures were as defined by PROMOTIF (Hutchinson and Thornton, 1996). Strands are colored green and the helices blue. Helix 4, which contains the active-site nucleophile Cys90, is colored cyan. This helix undergoes a severe kink, indeed PROMOTIF defines residues 90–100 and 103–105 as separate helices. We describe this as one continuous helix in order to maintain consistency of nomenclature with UCH-L3, which also has a severe kink in the corresponding part of helix 4. The following are labeled on the figure: strand 0 (S0, residues 11–12), strand 1 (S1, 31–36), strand 2 (S2, 54–60), strand 2^1 (S2^1, 81–82), strand 2^2 (S2^2, 128–129), strand 3 (S3, 165–172), strand 4 (S4, 176–180), strand 5 (S5, 189–193), strand 6 (S6, 227–233); helix 1 (H1, residues 15–25), helix 2 (H2, 44–46), helix 4 (H4, 90–105), helix 5 (H5, 111–122), helix 6 (H6, 132–143), helix 7 (H7, 205–221). Helices are alpha-type, except for helix 2 and residues 102–105 of helix 4, which adopt the 3[10] conformation. There is a turn of alpha helix (residues 146–150) within the active-site-crossover loop. (B) Same as (A), but including the Ubal shown in magenta. The sidechains of Ubal residues discussed in the text are shown in orange and labeled. Figures 1, 4, 5 and 6 were produced with the programs MOLSCRIPT (Kraulis, 1991) and RASTER 3D (Bacon and Anderson, 1988).

Figure 3.
Figure 3 Schematic of the UCH/cysteine protease reaction cycle. TI-1 and TI-2 denote the high energy tetrahedral intermediates; AI, the acyl intermediate; S, a cysteine; and Im, a histidine. Adapted from Storer and Ménard (1994).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 3877-3887) copyright 1999.

Figures were selected by the author.