PDBsum entry 2g4d

Hydrolase/protein binding

PDB id: 2g4d

Contents

Protein chains

205 a.a. *

78 a.a. *

Waters ×54

* Residue conservation analysis

PDB id:

2g4d

Name:

Hydrolase/protein binding

Title:

Crystal structure of human senp1 mutant (c603s) in complex with sumo-1

Structure:

Senp1 protein. Chain: a, c. Fragment: protease catalytic domain. Synonym: sentrin-specific protease 1. Engineered: yes. Mutation: yes. Small ubiquitin-related modifier 1. Chain: b, d. Fragment: residues 20-97.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

2.80Å R-factor: 0.248 R-free: 0.278

Authors:

Z.Xu,S.F.Chau,K.H.Lam,S.W.N.Au

Key ref:

Z.Xu et al. (2006). Crystal structure of the SENP1 mutant C603S-SUMO complex reveals the hydrolytic mechanism of SUMO-specific protease. Biochem J, 398, 345-352. PubMed id: 16712526

Date:

22-Feb-06 Release date: 17-Oct-06

Protein chains

Q9P0U3  (SENP1_HUMAN) -  Sentrin-specific protease 1 from Homo sapiens

Seq: 644 a.a.

Struc: 205 a.a.*

Protein chains

P63165  (SUMO1_HUMAN) -  Small ubiquitin-related modifier 1 from Homo sapiens

Seq: 101 a.a.

Struc: 78 a.a.

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

Enzyme reactions

• Enzyme class 2: Chains A, C: E.C.3.4.22.- - ?????
• Enzyme class 3: Chains B, D: E.C.?

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.

Biochem J 398:345-352 (2006)

PubMed id: 16712526

Crystal structure of the SENP1 mutant C603S-SUMO complex reveals the hydrolytic mechanism of SUMO-specific protease.

Z.Xu, S.F.Chau, K.H.Lam, H.Y.Chan, T.B.Ng, S.W.Au.

ABSTRACT

SUMO (small ubiquitin-related modifier)-specific proteases catalyse the maturation and de-conjugation processes of the sumoylation pathway and modulate various cellular responses including nuclear metabolism and cell cycle progression. The active-site cysteine residue is conserved among all known SUMO-specific proteases and is not substitutable by serine in the hydrolysis reactions demonstrated previously in yeast. We report here that the catalytic domain of human protease SENP1 (SUMO-specific protease 1) mutant SENP1C(C603S) carrying a mutation of cysteine to serine at the active site is inactive in maturation and de-conjugation reactions. To further understand the hydrolytic mechanism catalysed by SENP1, we have determined, at 2.8 A resolution (1 A = 0.1 nm), the X-ray structure of SENP1C(C603S)-SUMO-1 complex. A comparison of the structure of SENP2-SUMO-1 suggests strongly that SUMO-specific proteases require a self-conformational change prior to cleavage of peptide or isopeptide bond in the maturation and de-conjugation processes respectively. Moreover, analysis of the interface of SENP1 and SUMO-1 has led to the identification of four unique amino acids in SENP1 that facilitate the binding of SUMO-1. By means of an in vitro assay, we further demonstrate a novel function of SENP1 in hydrolysing the thioester linkage in E1-SUMO and E2-SUMO complexes. The results disclose a new mechanism of regulation of the sumoylation pathway by the SUMO-specific proteases.