PDBsum entry 3znh

Hydrolase/signaling protein

PDB id: 3znh

Contents

Protein chains

153 a.a.

76 a.a.

Waters ×48

PDB id:

3znh

Name:

Hydrolase/signaling protein

Title:

Crimean congo hemorrhagic fever virus otu domain in complex with ubiquitin-propargyl.

Structure:

Ubiquitin thioesterase. Chain: a. Fragment: otu domain, residues 1-183. Synonym: otu domain of crimean congo hemorrhagic fever virus cchfv. Engineered: yes. Polyubiquitin-b. Chain: b. Synonym: ubiquitin propargyl, ubiquitin. Engineered: yes.

Source:

Crimean-congo hemorrhagic fever virus. Organism_taxid: 652961. Strain: ibar10200. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: rosetta2 placi. Other_details: DNA generated by gene synthesis. Synthetic: yes. Homo sapiens.

Resolution:

2.30Å R-factor: 0.214 R-free: 0.275

Authors:

R.Ekkebus,S.I.Vankasteren,Y.Kulathu,A.Scholten,I.Berlin,A.Dejong, G.Goerdayal,J.Neefjes,A.J.R.Heck,D.Komander,H.Ovaa

Key ref:

R.Ekkebus et al. (2013). On terminal alkynes that can react with active-site cysteine nucleophiles in proteases. J Am Chem Soc, 135, 2867-2870. PubMed id: 23387960 DOI: 10.1021/ja309802n

Date:

14-Feb-13 Release date: 27-Feb-13

Protein chain

Q6TQR6  (L_CCHFI) -  RNA-directed RNA polymerase L from Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)

Seq: 3945 a.a.

Struc: 153 a.a.

Protein chain

P0CG47  (UBB_HUMAN) -  Polyubiquitin-B from Homo sapiens

Seq: 229 a.a.

Struc: 76 a.a.*

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

Enzyme reactions

• Enzyme class 2: Chain A: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: Chain A: E.C.3.1.-.-
• Enzyme class 4: Chain A: E.C.3.4.19.12 - ubiquitinyl hydrolase 1.
• 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).
• Enzyme class 5: Chain A: E.C.3.4.22.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

DOI no: 10.1021/ja309802n

J Am Chem Soc 135:2867-2870 (2013)

PubMed id: 23387960

On terminal alkynes that can react with active-site cysteine nucleophiles in proteases.

R.Ekkebus, S.I.van Kasteren, Y.Kulathu, A.Scholten, I.Berlin, P.P.Geurink, A.de Jong, S.Goerdayal, J.Neefjes, A.J.Heck, D.Komander, H.Ovaa.

ABSTRACT

Active-site directed probes are powerful in studies of enzymatic function. We report an active-site directed probe based on a warhead so far considered unreactive. By replacing the C-terminal carboxylate of ubiquitin (Ub) with an alkyne functionality, a selective reaction with the active-site cysteine residue of de-ubiquitinating enzymes was observed. The resulting product was shown to be a quaternary vinyl thioether, as determined by X-ray crystallography. Proteomic analysis of proteins bound to an immobilized Ub alkyne probe confirmed the selectivity toward de-ubiquitinating enzymes. The observed reactivity is not just restricted to propargylated Ub, as highlighted by the selective reaction between caspase-1 (interleukin converting enzyme) and a propargylated peptide derived from IL-1β, a caspase-1 substrate.