PDBsum entry 3jw0

Ligase/signaling protein

PDB id: 3jw0

Contents

Protein chains

146 a.a. *

376 a.a. *

76 a.a. *

Waters ×19

* Residue conservation analysis

PDB id:

3jw0

Name:

Ligase/signaling protein

Title:

E2~ubiquitin-hect

Structure:

Ubiquitin-conjugating enzyme e2 d2. Chain: a, b. Synonym: ubiquitin-protein ligase d2, ubiquitin carrier protein d2, ubiquitin-conjugating enzyme e2-17 kda 2, e2(17)kb 2. Engineered: yes. Mutation: yes. E3 ubiquitin-protein ligase nedd4-like. Chain: c, d. Fragment: nedd4l hect domain (unp 576-955).

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ube2d2, ubc4, ubch5b. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: nedd4l, kiaa0439, nedl3. Gene: rps27a, uba80, ubcep1, uba52, ubcep2, ubb, ubc.

Resolution:

3.10Å R-factor: 0.252 R-free: 0.287

Authors:

H.B.Kamadurai,B.A.Schulman

Key ref:

H.B.Kamadurai et al. (2009). Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex. Mol Cell, 36, 1095-1102. PubMed id: 20064473

Date:

17-Sep-09 Release date: 12-Jan-10

Protein chains

P62837  (UB2D2_HUMAN) -  Ubiquitin-conjugating enzyme E2 D2 from Homo sapiens

Seq: 147 a.a.

Struc: 146 a.a.*

Protein chains

Q96PU5  (NED4L_HUMAN) -  E3 ubiquitin-protein ligase NEDD4-like from Homo sapiens

Seq: 975 a.a.

Struc: 376 a.a.*

Protein chains

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 76 a.a.

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B: 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
• Enzyme class 3: Chains A, B: E.C.2.3.2.24 - (E3-independent) E2 ubiquitin-conjugating enzyme.
• Reaction: S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E1 ubiquitin-activating enzyme]-L-cysteine + N₆- monoubiquitinyl-[acceptor protein]-L-lysine
• Enzyme class 4: Chains C, D: E.C.2.3.2.26 - HECT-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 5: Chains C, D: E.C.2.3.2.36 - RING-type E3 ubiquitin transferase (cysteine targeting).
• Reaction: [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-cysteine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-S-ubiquitinyl-L-cysteine

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.

Mol Cell 36:1095-1102 (2009)

PubMed id: 20064473

Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex.

H.B.Kamadurai, J.Souphron, D.C.Scott, D.M.Duda, D.J.Miller, D.Stringer, R.C.Piper, B.A.Schulman.

ABSTRACT

In E1-E2-E3 ubiquitin (Ub) conjugation cascades, the E2 first forms a transient E2 approximately Ub covalent complex and then interacts with an E3 for Ub transfer. For cascades involving E3s in the HECT class, Ub is transferred from an associated E2 to the acceptor cysteine in the HECT domain C lobe. To gain insights into this process, we determined the crystal structure of a complex between the HECT domain of NEDD4L and the E2 UbcH5B bearing a covalently linked Ub at its active site (UbcH5B approximately Ub). Noncovalent interactions between UbcH5B and the HECT N lobe and between Ub and the HECT domain C lobe lead to an overall compact structure, with the Ub C terminus sandwiched between UbcH5B and HECT domain active sites. The structure suggests a model for E2-to-HECT Ub transfer, in which interactions between a donor Ub and an acceptor domain constrain upstream and downstream enzymes for conjugation.