PDBsum entry 3dbh

Cell cycle

PDB id: 3dbh

Contents

Protein chains

522 a.a. *

432 a.a. *

86 a.a. *

76 a.a. *

Metals

_ZN ×4

* Residue conservation analysis

PDB id:

3dbh

Name:

Cell cycle

Title:

Structural dissection of a gating mechanism preventing misactivation of ubiquitin by nedd8's e1 (appbp1-uba3arg190ala-nedd8ala72arg)

Structure:

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

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: nae1, appbp1. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: uba3, ube1c. Gene: nedd8.

Resolution:

2.85Å R-factor: 0.224 R-free: 0.274

Authors:

J.Souphron,B.A.Schulman

Key ref:

J.Souphron et al. (2008). Structural dissection of a gating mechanism preventing misactivation of ubiquitin by NEDD8's E1. Biochemistry, 47, 8961-8969. PubMed id: 18652489

Date:

31-May-08 Release date: 12-Aug-08

Protein chains

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

Seq: 534 a.a.

Struc: 522 a.a.

Protein chains

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

Seq: 463 a.a.

Struc: 432 a.a.*

Protein chain

Q15843  (NEDD8_HUMAN) -  NEDD8 from Homo sapiens

Seq: 81 a.a.

Struc: 86 a.a.*

Protein chains

Q15843  (NEDD8_HUMAN) -  NEDD8 from Homo sapiens

Seq: 81 a.a.

Struc: 76 a.a.*

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

Enzyme reactions

• Enzyme class: Chains B, D, F, H: 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

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

reference

Biochemistry 47:8961-8969 (2008)

PubMed id: 18652489

Structural dissection of a gating mechanism preventing misactivation of ubiquitin by NEDD8's E1.

J.Souphron, M.B.Waddell, A.Paydar, Z.Tokgöz-Gromley, M.F.Roussel, B.A.Schulman.

ABSTRACT

Post-translational covalent modification by ubiquitin and ubiquitin-like proteins (UBLs) is a major eukaryotic mechanism for regulating protein function. In general, each UBL has its own E1 that serves as the entry point for a cascade. The E1 first binds the UBL and catalyzes adenylation of the UBL's C-terminus, prior to promoting UBL transfer to a downstream E2. Ubiquitin's Arg 72, which corresponds to Ala72 in the UBL NEDD8, is a key E1 selectivity determinant: swapping ubiquitin and NEDD8 residue 72 identity was shown previously to swap their E1 specificity. Correspondingly, Arg190 in the UBA3 subunit of NEDD8's heterodimeric E1 (the APPBP1-UBA3 complex), which corresponds to a Gln in ubiquitin's E1 UBA1, is a key UBL selectivity determinant. Here, we dissect this specificity with biochemical and X-ray crystallographic analysis of APPBP1-UBA3-NEDD8 complexes in which NEDD8's residue 72 and UBA3's residue 190 are substituted with different combinations of Ala, Arg, or Gln. APPBP1-UBA3's preference for NEDD8's Ala72 appears to be indirect, due to proper positioning of UBA3's Arg190. By contrast, our data are consistent with direct positive interactions between ubiquitin's Arg72 and an E1's Gln. However, APPBP1-UBA3's failure to interact with a UBL having Arg72 is not due to a lack of this favorable interaction, but rather arises from UBA3's Arg190 acting as a negative gate. Thus, parallel residues from different UBL pathways can utilize distinct mechanisms to dictate interaction selectivity, and specificity can be amplified by barriers that prevent binding to components of different conjugation cascades.