PDBsum entry 2qho

Protein binding/ligase

PDB id: 2qho

Contents

Protein chains

72 a.a. *

47 a.a. *

76 a.a. *

49 a.a. *

49 a.a. *

Waters ×304

* Residue conservation analysis

PDB id:

2qho

Name:

Protein binding/ligase

Title:

Crystal structure of the uba domain from edd ubiquitin ligase in complex with ubiquitin

Structure:

Ubiquitin. Chain: a, c, e, g. E3 ubiquitin-protein ligase edd1. Chain: b, d, f, h. Fragment: residues 180-230. Synonym: hyperplastic discs protein homolog, hhyd, progestin-induced protein. Engineered: yes

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Homo sapiens. Human. Organism_taxid: 9606. Gene: edd1, edd, hyd, kiaa0896. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

1.85Å R-factor: 0.209 R-free: 0.258

Authors:

G.Kozlov,K.Gehring

Key ref:

G.Kozlov et al. (2007). Structural basis of ubiquitin recognition by the ubiquitin-associated (UBA) domain of the ubiquitin ligase EDD. J Biol Chem, 282, 35787-35795. PubMed id: 17897937 DOI: 10.1074/jbc.M705655200

Date:

02-Jul-07 Release date: 25-Sep-07

Protein chains

P0CH28  (UBC_BOVIN) -  Polyubiquitin-C from Bos taurus

Seq: 690 a.a.

Struc: 72 a.a.

Protein chain

O95071  (UBR5_HUMAN) -  E3 ubiquitin-protein ligase UBR5 from Homo sapiens

Seq: 2799 a.a.

Struc: 47 a.a.*

Protein chains

P0CH28  (UBC_BOVIN) -  Polyubiquitin-C from Bos taurus

Seq: 690 a.a.

Struc: 76 a.a.

Protein chains

O95071  (UBR5_HUMAN) -  E3 ubiquitin-protein ligase UBR5 from Homo sapiens

Seq: 2799 a.a.

Struc: 49 a.a.*

Protein chain

O95071  (UBR5_HUMAN) -  E3 ubiquitin-protein ligase UBR5 from Homo sapiens

Seq: 2799 a.a.

Struc: 49 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains A, C, E, G: E.C.?
• Enzyme class 2: Chains B, D, F, H: 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

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.

DOI no: 10.1074/jbc.M705655200

J Biol Chem 282:35787-35795 (2007)

PubMed id: 17897937

Structural basis of ubiquitin recognition by the ubiquitin-associated (UBA) domain of the ubiquitin ligase EDD.

G.Kozlov, L.Nguyen, T.Lin, G.De Crescenzo, M.Park, K.Gehring.

ABSTRACT

EDD (or HYD) is an E3 ubiquitin ligase in the family of HECT (homologous to E6-AP C terminus) ligases. EDD contains an N-terminal ubiquitin-associated (UBA) domain, which is present in a variety of proteins involved in ubiquitin-mediated processes. Here, we use isothermal titration calorimetry (ITC), NMR titrations, and pull-down assays to show that the EDD UBA domain binds ubiquitin. The 1.85 A crystal structure of the complex with ubiquitin reveals the structural basis of ubiquitin recognition by UBA helices alpha1 and alpha3. The structure shows a larger number of intermolecular hydrogen bonds than observed in previous UBA/ubiquitin complexes. Two of these involve ordered water molecules. The functional importance of residues at the UBA/ubiquitin interface was confirmed using site-directed mutagenesis. Surface plasmon resonance (SPR) measurements show that the EDD UBA domain does not have a strong preference for polyubiquitin chains over monoubiquitin. This suggests that EDD binds to monoubiquitinated proteins, which is consistent with its involvement in DNA damage repair pathways.

Selected figure(s)

Figure 1.
FIGURE 1. The UBA domain of EDD binds to ubiquitin and polyubiquitin. A, in vitro binding of the EDD and Cbl-b UBA domains to ubiquitin agarose. B, in vitro binding of the EDD and Cbl-b UBA domain to ubiquitin chains. C, calorimetric titration of the EDD UBA domain with ubiquitin. The panel shows the integrated heat released after correction for the heat of dilution (data points, squares) and the curve of best fit for binding to a single site.

Figure 4.
FIGURE 4. Crystal structure of the EDD UBA-ubiquitin complex. A, overall structure of the complex. Ubiquitin is in yellow, and the UBA domain is in purple. B, UBA Val^196 binds the hydrophobic groove formed by Ile^44, His^68, and Val^70 of ubiquitin. C, UBA Leu^224 binds the groove formed by Ile^44, Arg^42, Gln^49, and Val^70 of ubiquitin. D, Arg^42 and Gln^49 of ubiquitin form a network of intermolecular hydrogen bonds with Asn^221 and Ser^225 of EDD UBA. E, amide of Gly^47 of ubiquitin forms an intermolecular hydrogen bond with carbonyl of Val^216 of EDD UBA via a bound water molecule. F, bound water molecule facilitates hydrogen bonding between amide of Leu^71 of ubiquitin and side chain of Asn^217 of EDD UBA. The 2F[o]-F[c] electron density (1 contour, omit map) for bound water molecules is shown in panels E and F.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 35787-35795) copyright 2007.

Figures were selected by the author.