PDBsum entry: 1nbf

Hydrolase

PDB id: 1nbf

Contents

Protein chains

347 a.a. *

76 a.a. *

Waters ×374

* Residue conservation analysis

PDB id:

1nbf

Name:

Hydrolase

Title:

Crystal structure of a ubp-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde

Structure:

Ubiquitin carboxyl-terminal hydrolase 7. Chain: a, b, e. Fragment: hausp core domain. Synonym: deubiquitinating enzyme 7. Engineered: yes. Ubiquitin aldehyde. Chain: c, d. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: usp7. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: uba52. Expression_system_taxid: 562

Biol. unit:

Monomer (from PQS)

Resolution:

2.30Å R-factor: 0.218 R-free: 0.262

Authors:

M.Hu,P.Li,M.Li,W.Li,T.Yao,J.-W.Wu,W.Gu,R.E.Cohen,Y.Shi

Key ref:

M.Hu et al. (2002). Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde. Cell, 111, 1041-1054. PubMed id: 12507430 DOI: 10.1016/S0092-8674(02)01199-6

Date:

02-Dec-02 Release date: 07-Jan-03

Protein chains

Q93009  (UBP7_HUMAN) -  Ubiquitin carboxyl-terminal hydrolase 7

Seq: 1102 a.a.

Struc: 347 a.a.

Protein chains

P62979  (RS27A_HUMAN) -  Ubiquitin-40S ribosomal protein S27a

Seq: 156 a.a.

Struc: 76 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, B, E: E.C.3.1.2.15 - Ubiquitin thiolesterase.
• Reaction: Ubiquitin C-terminal thioester + H₂O = ubiquitin + a thiol

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: ubiquitin-dependent protein catabolic process (1 term)
• Biochemical function: ubiquitin thiolesterase activity (1 term)

Key reference

DOI no: 10.1016/S0092-8674(02)01199-6

Cell 111:1041-1054 (2002)

PubMed id: 12507430

Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde.

M.Hu, P.Li, M.Li, W.Li, T.Yao, J.W.Wu, W.Gu, R.E.Cohen, Y.Shi.

ABSTRACT

The ubiquitin-specific processing protease (UBP) family of deubiquitinating enzymes plays an essential role in numerous cellular processes. HAUSP, a representative UBP, specifically deubiquitinates and hence stabilizes the tumor suppressor protein p53. Here, we report the crystal structures of the 40 kDa catalytic core domain of HAUSP in isolation and in complex with ubiquitin aldehyde. These studies reveal that the UBP deubiquitinating enzymes exhibit a conserved three-domain architecture, comprising Fingers, Palm, and Thumb. The leaving ubiquitin moiety is specifically coordinated by the Fingers, with its C terminus placed in the active site between the Palm and the Thumb. Binding by ubiquitin aldehyde induces a drastic conformational change in the active site that realigns the catalytic triad residues for catalysis.

Selected figure(s)

Figure 4.
Figure 4. Specific Interactions between HAUSP and Ubal(A) A large conformational change at the active site induced by Ubal binding. The active sites of HAUSP in isolation (purple) and in complex with Ubal (blue) are superimposed and shown in stereo. The C-terminal tail of Ubal is shown in green. The catalytic triad residues and Asn218 are shown. Note the dramatic conformational changes on all three catalytic residues, which realign these residues for productive catalysis. Hydrogen bonds are represented by red dashed lines.(B) A stereo view of the hydrogen bonds between HAUSP and the C terminus of Ubal. A water molecule, marked by the letter w, likely plays an important role by hydrogen bonding to the oxyanion and two surrounding residues (Asn218 and Asp482).(C) A stereo view of the van der Waals interactions between HAUSP and the C terminus of Ubal. The side chains of the Ubal C-terminal six residues as well as several critical HAUSP residues are shown.(D) A stereo view of the interactions between the tip of the Fingers in HAUSP and Ubal. All HAUSP residues shown in (A–D) are highly conserved among all members of UBPs.(E) Deubiquitination activity of mutant HAUSP proteins. The substrate used in this assay is Lys48-linked diubiquitin. The role of the affected residue is briefly indicated. HHAA represents the double mutation H456A/H464A. Mutation of any catalytically important residue leads to complete abolishment of the deubiquitination activity.

Figure 5.
Figure 5. Structural Comparison of HAUSP-Ubal with Yuh1-Ubal and Ulp-Smt3 Complexes(A) Superposition of the structure of the HAUSP-Ubal complex with that of Yuh1-Ubal. These two structures are aligned on their deubiquitination domains. HAUSP and Yuh1 are shown in blue and purple, respectively. The HAUSP- and Yuh1-associated Ubal moieties are represented as transparent surfaces colored green and yellow, respectively. Two perpendicular views are shown.(B) Stereo comparison of the active sites of HAUSP (blue) and Yuh1 (purple). The C-terminal tails of Ubal is shown in green and yellow for the HAUSP and Yuh1 complexes, respectively. Catalytic triad residues and the oxyanion-coordinating residue are shown. Hydrogen bonds are represented by red dashed lines. The catalytic triad residues are superimposed with a rmsd of 0.23 Å.(C) Stereo comparison of the active sites of HAUSP (blue) and Ulp1 (gold). The C-terminal tails of Ubal and Smt3 (SUMO homolog in yeast) are shown in green and yellow, respectively. Catalytic triad residues and the oxyanion-coordinating residue are shown.

The above figures are reprinted by permission from Cell Press: Cell (2002, 111, 1041-1054) copyright 2002.

Figures were selected by an automated process.