PDBsum entry 3gzn

Protein binding/ligase

PDB id: 3gzn

Contents

Protein chains

527 a.a. *

429 a.a. *

79 a.a. *

Ligands

B39 ×2

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

3gzn

Name:

Protein binding/ligase

Title:

Structure of nedd8-activating enzyme in complex with nedd8 and mln4924

Structure:

Nedd8-activating enzyme e1 regulatory subunit. Chain: a, c. Synonym: amyloid protein-binding protein 1, amyloid beta precursor protein-binding protein 1, 59 kda, app-bp1, proto-oncogene protein 1. Engineered: yes. Nedd8-activating enzyme e1 catalytic subunit. Chain: b, d. Synonym: ubiquitin-like modifier-activating enzyme 3, ubiquitin- activating enzyme 3, nedd8-activating enzyme e1c, ubiquitin-

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: appbp1, hpp1, nae1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Gene: uba3, ube1c. Gene: nedd8.

Resolution:

3.00Å R-factor: 0.233 R-free: 0.287

Authors:

M.D.Sintchak

Key ref:

J.E.Brownell et al. (2010). Substrate-assisted inhibition of ubiquitin-like protein-activating enzymes: the NEDD8 E1 inhibitor MLN4924 forms a NEDD8-AMP mimetic in situ. Mol Cell, 37, 102-111. PubMed id: 20129059

Date:

07-Apr-09 Release date: 02-Feb-10

Protein chains

Q13564  (ULA1_HUMAN) -  NEDD8-activating enzyme E1 regulatory subunit from Homo sapiens

Seq: 534 a.a.

Struc: 527 a.a.

Protein chains

Q8TBC4  (UBA3_HUMAN) -  NEDD8-activating enzyme E1 catalytic subunit from Homo sapiens

Seq: 463 a.a.

Struc: 429 a.a.

Protein chains

Q15843  (NEDD8_HUMAN) -  NEDD8 from Homo sapiens

Seq: 81 a.a.

Struc: 79 a.a.

Enzyme reactions

• Enzyme class: Chains B, D: E.C.6.2.1.64 - E1 NEDD8-activating enzyme.
• Reaction: ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine = AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L- cysteine

ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine = AMP (Bound ligand (Het Group name = B39) matches with 42.11% similarity) + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L- cysteine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Mol Cell 37:102-111 (2010)

PubMed id: 20129059

Substrate-assisted inhibition of ubiquitin-like protein-activating enzymes: the NEDD8 E1 inhibitor MLN4924 forms a NEDD8-AMP mimetic in situ.

J.E.Brownell, M.D.Sintchak, J.M.Gavin, H.Liao, F.J.Bruzzese, N.J.Bump, T.A.Soucy, M.A.Milhollen, X.Yang, A.L.Burkhardt, J.Ma, H.K.Loke, T.Lingaraj, D.Wu, K.B.Hamman, J.J.Spelman, C.A.Cullis, S.P.Langston, S.Vyskocil, T.B.Sells, W.D.Mallender, I.Visiers, P.Li, C.F.Claiborne, M.Rolfe, J.B.Bolen, L.R.Dick.

ABSTRACT

The NEDD8-activating enzyme (NAE) initiates a protein homeostatic pathway essential for cancer cell growth and survival. MLN4924 is a selective inhibitor of NAE currently in clinical trials for the treatment of cancer. Here, we show that MLN4924 is a mechanism-based inhibitor of NAE and creates a covalent NEDD8-MLN4924 adduct catalyzed by the enzyme. The NEDD8-MLN4924 adduct resembles NEDD8 adenylate, the first intermediate in the NAE reaction cycle, but cannot be further utilized in subsequent intraenzyme reactions. The stability of the NEDD8-MLN4924 adduct within the NAE active site blocks enzyme activity, thereby accounting for the potent inhibition of the NEDD8 pathway by MLN4924. Importantly, we have determined that compounds resembling MLN4924 demonstrate the ability to form analogous adducts with other ubiquitin-like proteins (UBLs) catalyzed by their cognate-activating enzymes. These findings reveal insights into the mechanism of E1s and suggest a general strategy for selective inhibition of UBL conjugation pathways.