PDBsum entry 2dq5

Ligase

PDB id: 2dq5

Contents

Protein chain

47 a.a. *

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

2dq5

Name:

Ligase

Title:

Solution structure of the mid1 b box2 chc(d/c)c2h2 zinc-binding domain: insights into an evolutionary conserved ring fold

Structure:

Midline-1. Chain: a. Fragment: bbox2 domain. Synonym: tripartite motif protein 18, putative transcription factor xprf, midin, ring finger protein 59, midline 1 ring finger protein. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: mid1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

16 models

Authors:

M.A.Massiah,J.A.B.Matts,K.M.Short,B.N.Simmons,S.Singireddy,J.Zou, T.C.Cox

Key ref:

M.A.Massiah et al. (2007). Solution Structure of the MID1 B-box2 CHC(D/C)C(2)H(2) Zinc-binding Domain: Insights into an Evolutionarily Conserved RING Fold. J Mol Biol, 369, 1. PubMed id: 17428496 DOI: 10.1016/j.jmb.2007.03.017

Date:

20-May-06 Release date: 03-Apr-07

Protein chain

O15344  (TRI18_HUMAN) -  E3 ubiquitin-protein ligase Midline-1 from Homo sapiens

Seq: 667 a.a.

Struc: 47 a.a.

Enzyme reactions

• Enzyme class: 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

DOI no: 10.1016/j.jmb.2007.03.017

J Mol Biol 369:1 (2007)

PubMed id: 17428496

Solution Structure of the MID1 B-box2 CHC(D/C)C(2)H(2) Zinc-binding Domain: Insights into an Evolutionarily Conserved RING Fold.

M.A.Massiah, J.A.Matts, K.M.Short, B.N.Simmons, S.Singireddy, Z.Yi, T.C.Cox.

ABSTRACT

The B-box type 2 domain is a prominent feature of a large and growing family of RING, B-box, coiled-coil (RBCC) domain-containing proteins and is also present in more than 1500 additional proteins. Most proteins usually contain a single B-box2 domain, although some proteins contain tandem domains consisting of both type 1 and type 2 B-boxes, which actually share little sequence similarity. Recently, we determined the solution structure of B-box1 from MID1, a putative E3 ubiquitin ligase that is mutated in X-linked Opitz G/BBB syndrome, and showed that it adopted a betabetaalpha RING-like fold. Here, we report the tertiary structure of the B-box2 (CHC(D/C)C(2)H(2)) domain from MID1 using multidimensional NMR spectroscopy. This MID1 B-box2 domain consists of a short alpha-helix and a structured loop with two short anti-parallel beta-strands and adopts a tertiary structure similar to the B-box1 and RING structures, even though there is minimal primary sequence similarity between these domains. By mutagenesis, ESI-FTICR and ICP mass spectrometry, we show that the B-box2 domain coordinates two zinc atoms with a 'cross-brace' pattern: one by Cys175, His178, Cys195 and Cys198 and the other by Cys187, Asp190, His204, and His207. Interestingly, this is the first case that an aspartic acid is involved in zinc atom coordination in a zinc-finger domain, although aspartic acid has been shown to coordinate non-catalytic zinc in matrix metalloproteinases. In addition, the finding of a Cys195Phe substitution identified in a patient with X-linked Opitz GBBB syndrome supports the importance of proper zinc coordination for the function of the MID1 B-box2 domain. Notably, however, our structure differs from the only other published B-box2 structure, that from XNF7, which was shown to coordinate one zinc atom. Finally, the similarity in tertiary structures of the B-box2, B-box1 and RING domains suggests these domains have evolved from a common ancestor.

Selected figure(s)

Figure 2.
Figure 2. A surface representation of the B-box2 domain. (a) The surface of the MID1 B-box2 domain showing basic patches (colored blue) comprised of lysine and arginine residues, acidic patches (colored red) of glutamic and aspartic acid residues, and hydrophobic patches (colored green) formed by leucine, isoleucine, alanine, tyrosine, methionine, and valine. All other residues are white. Two spheres representing the two zinc atoms and a ribbon drawing of B-box2 are depicted. Note the extensive hydrophobic surface on the outer surface of the helix and structured loop with the β-strands. This pattern of hydrophobic surfaces and distinct charge patches is similar in the other B-box2 domains, except TRIM29. (b) Hydrophobic and charge distribution of TRIM29 B-box2, shown in the same orientation as MID1 B-box2 in (a) (left). The other side of TRIM29 B-box2 (not shown) is predominately hydrophobic. Notably, the surface above the structured loop with the two β-strands is hydrophobic, similar to MID1 B-box2; however, a C-terminal helix packs against this surface, suggesting a possible domain–domain interface. (c) The superposition of MID1 B-box1 (green) and B-box2 (red) showing the overall similarity in secondary and tertiary structures, even though their primary sequences are not homologous. The relative locations of the zinc ions (shown as green and red balls) are also similar.

Figure 3.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 369, 1-0) copyright 2007.

Figures were selected by an automated process.