PDBsum entry 5n4w

Ligase

PDB id: 5n4w

Contents

Protein chains

671 a.a.

37 a.a.

86 a.a.

82 a.a.

91 a.a.

Metals

_ZN ×3

PDB id:

5n4w

Name:

Ligase

Title:

Crystal structure of the cul2-rbx1-elobc-vhl ubiquitin ligase complex

Structure:

Cullin-2. Chain: a. Synonym: cul-2. Engineered: yes. Von hippel-lindau disease tumor suppressor. Chain: v. Synonym: protein g7,pvhl. Engineered: yes. E3 ubiquitin-protein ligase rbx1.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cul2. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf21. Gene: vhl. Expressed in: escherichia coli.

Resolution:

3.90Å R-factor: 0.304 R-free: 0.346

Authors:

T.A.F.Cardote,M.S.Gadd,A.Ciulli

Key ref:

T.A.F.Cardote et al. (2017). Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex. Structure, 25, 901. PubMed id: 28591624

Date:

11-Feb-17 Release date: 07-Jun-17

Protein chain

Q13617  (CUL2_HUMAN) -  Cullin-2 from Homo sapiens

Seq: 745 a.a.

Struc: 671 a.a.*

Protein chain

P40337  (VHL_HUMAN) -  von Hippel-Lindau disease tumor suppressor from Homo sapiens

Seq: 213 a.a.

Struc: 37 a.a.

Protein chain

P62877  (RBX1_HUMAN) -  E3 ubiquitin-protein ligase RBX1 from Homo sapiens

Seq: 108 a.a.

Struc: 86 a.a.*

Protein chain

Q15370  (ELOB_HUMAN) -  Elongin-B from Homo sapiens

Seq: 118 a.a.

Struc: 82 a.a.

Protein chain

Q15369  (ELOC_HUMAN) -  Elongin-C from Homo sapiens

Seq: 112 a.a.

Struc: 91 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, V, B, C: E.C.?
• Enzyme class 3: Chain R: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine
• Enzyme class 4: Chain R: E.C.2.3.2.32 - cullin-RING-type E3 NEDD8 transferase.
• Reaction: S-[NEDD8-protein]-yl-[E2 NEDD8-conjugating enzyme]-L-cysteine + [cullin]- L-lysine = [E2 NEDD8-conjugating enzyme]-L-cysteine + N₆-[NEDD8- protein]-yl-[cullin]-L-lysine

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.

Structure 25:901 (2017)

PubMed id: 28591624

Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex.

T.A.F.Cardote, M.S.Gadd, A.Ciulli.

ABSTRACT

Cullin RING E3 ubiquitin ligases (CRLs) function in the ubiquitin proteasome system to catalyze the transfer of ubiquitin from E2 conjugating enzymes to specific substrate proteins. CRLs are large dynamic complexes and attractive drug targets for the development of small-molecule inhibitors and chemical inducers of protein degradation. The atomic details of whole CRL assembly and interactions that dictate subunit specificity remain elusive. Here we present the crystal structure of a pentameric CRL2^VHLcomplex, composed of Cul2, Rbx1, Elongin B, Elongin C, and pVHL. The structure traps a closed state of full-length Cul2 and a new pose of Rbx1 in a trajectory from closed to open conformation. We characterize hotspots and binding thermodynamics at the interface between Cul2 and pVHL-EloBC and identify mutations that contribute toward a selectivity switch for Cul2 versus Cul5 recognition. Our findings provide structural and biophysical insights into the whole Cul2 complex that could aid future drug targeting.