PDBsum entry 3b0a

Signaling protein/metal binding protein

PDB id: 3b0a

Contents

Protein chains

151 a.a.

57 a.a.

63 a.a.

Ligands

TAM

Metals

_ZN ×2

Waters ×319

PDB id:

3b0a

Name:

Signaling protein/metal binding protein

Title:

Crystal structure of the mouse hoil1-l-nzf in complex with linear di- ubiquitin

Structure:

Polyubiquitin-c. Chain: a, d. Fragment: linear di ubiquitin, unp residues 1-152. Synonym: ubiquitin. Engineered: yes. Ranbp-type and c3hc4-type zinc finger-containing protein 1. Chain: b, e. Fragment: unp residues 192-250. Synonym: heme-oxidized irp2 ubiquitin ligase 1 homolog, hoil-1,

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ubc. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. Mouse. Organism_taxid: 10090.

Resolution:

1.90Å R-factor: 0.183 R-free: 0.227

Authors:

Y.Sato,H.Fujita,A.Yoshikawa,M.Yamashita,A.Yamagata,S.E.Kaiser,K.Iwai, S.Fukai

Key ref:

Y.Sato et al. (2011). Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex. Proc Natl Acad Sci U S A, 108, 20520-20525. PubMed id: 22139374

Date:

07-Jun-11 Release date: 14-Dec-11

Protein chains

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 151 a.a.

Protein chain

Q9WUB0  (HOIL1_MOUSE) -  RanBP-type and C3HC4-type zinc finger-containing protein 1 from Mus musculus

Seq: 508 a.a.

Struc: 57 a.a.*

Protein chain

Q9WUB0  (HOIL1_MOUSE) -  RanBP-type and C3HC4-type zinc finger-containing protein 1 from Mus musculus

Seq: 508 a.a.

Struc: 63 a.a.*

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

Enzyme reactions

• Enzyme class 1: Chains A, D: E.C.?
• Enzyme class 2: Chains B, E: E.C.2.3.2.31 - RBR-type E3 ubiquitin transferase.
• Reaction: [E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N₆-ubiquitinyl-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.

Proc Natl Acad Sci U S A 108:20520-20525 (2011)

PubMed id: 22139374

Specific recognition of linear ubiquitin chains by the Npl4 zinc finger (NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex.

Y.Sato, H.Fujita, A.Yoshikawa, M.Yamashita, A.Yamagata, S.E.Kaiser, K.Iwai, S.Fukai.

ABSTRACT

The linear ubiquitin chain assembly complex (LUBAC) is a key nuclear factor-κB (NF-κB) pathway component that produces linear polyubiquitin chains. The HOIL-1L subunit of LUBAC has been shown to bind linear chains; however, detailed structural and functional analyses on the binding between LUBAC and linear chains have not been performed. In this study, we found that the Npl4 zinc finger (NZF) domain of HOIL-1L specifically binds linear polyubiquitin chains and determined the crystal structure of the HOIL-1L NZF domain in complex with linear diubiquitin at 1.7-Å resolution. The HOIL-1L NZF domain consists of a zinc-coordinating "NZF core" region and an additional α-helical "NZF tail" region. The HOIL-1L NZF core binds both the canonical Ile44-centered hydrophobic surface on the distal ubiquitin and a Phe4-centered hydrophobic patch on the proximal ubiquitin, representing a mechanism for the specific recognition of linear chains. The NZF tail binds the proximal ubiquitin to enhance the binding affinity. These recognition mechanisms were supported by the accompanying in vitro and in vivo structure-based mutagenesis experiments.