PDBsum entry 5jp1

Hydrolase

PDB id: 5jp1

Contents

Protein chains

199 a.a.

78 a.a.

Ligands

MLI ×2

D1D

Waters ×199

PDB id:

5jp1

Name:

Hydrolase

Title:

Structure of xanthomonas campestris effector protein xopd bound to tomato sumo

Structure:

Xanthomonas outer protein d. Chain: a. Fragment: unp residues 298-515. Engineered: yes. Small ubiquitin-related modifier. Chain: b. Synonym: sumo. Engineered: yes

Source:

Xanthomonas campestris pv. Vesicatoria (strain 85-10). Organism_taxid: 316273. Gene: xopd, xcv0437. Expressed in: escherichia coli. Expression_system_taxid: 562. Solanum lycopersicum. Tomato. Organism_taxid: 4081.

Resolution:

2.10Å R-factor: 0.183 R-free: 0.217

Authors:

J.N.Pruneda,D.Komander

Key ref:

J.N.Pruneda et al. (2016). The Molecular Basis for Ubiquitin and Ubiquitin-like Specificities in Bacterial Effector Proteases. Mol Cell, 63, 261-276. PubMed id: 27425412 DOI: 10.1016/j.molcel.2016.06.015

Date:

03-May-16 Release date: 27-Jul-16

Protein chain

Q3BYJ5  (Q3BYJ5_XANE5) -  Xanthomonas outer protein D from Xanthomonas euvesicatoria pv. vesicatoria (strain 85-10)

Seq: 545 a.a.

Struc: 199 a.a.

Protein chain

Q9SMD1  (Q9SMD1_SOLLC) -  Small ubiquitin-related modifier from Solanum lycopersicum

Seq: 105 a.a.

Struc: 78 a.a.*

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

DOI no: 10.1016/j.molcel.2016.06.015

Mol Cell 63:261-276 (2016)

PubMed id: 27425412

The Molecular Basis for Ubiquitin and Ubiquitin-like Specificities in Bacterial Effector Proteases.

J.N.Pruneda, C.H.Durkin, P.P.Geurink, H.Ovaa, B.Santhanam, D.W.Holden, D.Komander.

ABSTRACT

Pathogenic bacteria rely on secreted effector proteins to manipulate host signaling pathways, often in creative ways. CE clan proteases, specific hydrolases for ubiquitin-like modifications (SUMO and NEDD8) in eukaryotes, reportedly serve as bacterial effector proteins with deSUMOylase, deubiquitinase, or, even, acetyltransferase activities. Here, we characterize bacterial CE protease activities, revealing K63-linkage-specific deubiquitinases in human pathogens, such as Salmonella, Escherichia, and Shigella, as well as ubiquitin/ubiquitin-like cross-reactive enzymes in Chlamydia, Rickettsia, and Xanthomonas. Five crystal structures, including ubiquitin/ubiquitin-like complexes, explain substrate specificities and redefine relationships across the CE clan. Importantly, this work identifies novel family members and provides key discoveries among previously reported effectors, such as the unexpected deubiquitinase activity in Xanthomonas XopD, contributed by an unstructured ubiquitin binding region. Furthermore, accessory domains regulate properties such as subcellular localization, as exemplified by a ubiquitin-binding domain in Salmonella Typhimurium SseL. Our work both highlights and explains the functional adaptations observed among diverse CE clan proteins.