PDBsum entry 6ulh

Transferase

PDB id: 6ulh

Contents

Protein chains

376 a.a.

145 a.a.

76 a.a.

Waters ×272

PDB id:

6ulh

Name:

Transferase

Title:

Structure of mavc in complex with its substrate in r3 spacegroup

Structure:

Lpg2147 (mavc). Chain: a. Engineered: yes. Mutation: yes. Ubiquitin-conjugating enzyme e2 n. Chain: c. Synonym: bendless-like ubiquitin-conjugating enzyme,e2 ubiquitin- conjugating enzyme n,ubc13,ubch13,ubiquitin carrier protein n, ubiquitin-protein ligase n.

Source:

Legionella pneumophila. Organism_taxid: 446. Gene: lpg2147. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Homo sapiens. Human. Organism_taxid: 9606. Gene: ube2n, blu.

Resolution:

1.97Å R-factor: 0.185 R-free: 0.227

Authors:

S.Iyer,K.Puvar,C.Das

Key ref:

K.Puvar et al. (2020). Legionella effector MavC targets the Ube2N~Ub conjugate for noncanonical ubiquitination. Nat Commun, 11, 2365. PubMed id: 32398758 DOI: 10.1038/s41467-020-16211-x

Date:

08-Oct-19 Release date: 27-May-20

Protein chain

Q5ZTL4  (Q5ZTL4_LEGPH) -  MvcA insertion domain-containing protein from Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)

Seq: 482 a.a.

Struc: 376 a.a.*

Protein chain

P61088  (UBE2N_HUMAN) -  Ubiquitin-conjugating enzyme E2 N from Homo sapiens

Seq: 152 a.a.

Struc: 145 a.a.

Protein chain

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 76 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chain C: E.C.2.3.2.23 - E2 ubiquitin-conjugating enzyme.
• Reaction: S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L- cysteine

DOI no: 10.1038/s41467-020-16211-x

Nat Commun 11:2365 (2020)

PubMed id: 32398758

Legionella effector MavC targets the Ube2N~Ub conjugate for noncanonical ubiquitination.

K.Puvar, S.Iyer, J.Fu, S.Kenny, K.I.Negrón Terón, Z.Q.Luo, P.S.Brzovic, R.E.Klevit, C.Das.

ABSTRACT

The bacterial effector MavC modulates the host immune response by blocking Ube2N activity employing an E1-independent ubiquitin ligation, catalyzing formation of a γ-glutamyl-ε-Lys (Gln40^Ub-Lys92^Ube2N) isopeptide crosslink using a transglutaminase mechanism. Here we provide biochemical evidence in support of MavC targeting the activated, thioester-linked Ube2N~ubiquitin conjugate, catalyzing an intramolecular transglutamination reaction, covalently crosslinking the Ube2N and Ub subunits effectively inactivating the E2~Ub conjugate. Ubiquitin exhibits weak binding to MavC alone, but shows an increase in affinity when tethered to Ube2N in a disulfide-linked substrate that mimics the charged E2~Ub conjugate. Crystal structures of MavC in complex with the substrate mimic and crosslinked product provide insights into the reaction mechanism and underlying protein dynamics that favor transamidation over deamidation, while revealing a crucial role for the structurally unique insertion domain in substrate recognition. This work provides a structural basis of ubiquitination by transglutamination and identifies this enzyme's true physiological substrate.