PDBsum entry 1p1a

DNA binding protein

PDB id: 1p1a

Contents

Protein chain

85 a.a. *

* Residue conservation analysis

PDB id:

1p1a

Name:

DNA binding protein

Title:

Nmr structure of ubiquitin-like domain of hhr23b

Structure:

Uv excision repair protein rad23 homolog b. Chain: a. Fragment: ubiquitin-like domain. Synonym: rad23, hhr23b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hhr23b. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

14 models

Authors:

K.S.Ryu,K.J.Lee,S.H.Bae,B.K.Kim,K.A.Kim,B.S.Choi

Key ref:

K.S.Ryu et al. (2003). Binding surface mapping of intra- and interdomain interactions among hHR23B, ubiquitin, and polyubiquitin binding site 2 of S5a. J Biol Chem, 278, 36621-36627. PubMed id: 12832454 DOI: 10.1074/jbc.M304628200

Date:

11-Apr-03 Release date: 13-Jul-04

Protein chain

P54727  (RD23B_HUMAN) -  UV excision repair protein RAD23 homolog B from Homo sapiens

Seq: 409 a.a.

Struc: 85 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1074/jbc.M304628200

J Biol Chem 278:36621-36627 (2003)

PubMed id: 12832454

Binding surface mapping of intra- and interdomain interactions among hHR23B, ubiquitin, and polyubiquitin binding site 2 of S5a.

K.S.Ryu, K.J.Lee, S.H.Bae, B.K.Kim, K.A.Kim, B.S.Choi.

ABSTRACT

hHR23B is the human homologue of the yeast protein RAD23 and is known to participate in DNA repair by stabilizing xeroderma pigmentosum group C protein. However, hHR23B and RAD23 also have many important functions related to general proteolysis. hHR23B consists of N-terminal ubiquitin-like (UbL), ubiquitin association 1 (UBA1), xeroderma pigmentosum group C binding, and UBA2 domains. The UBA domains interact with ubiquitin (Ub) and inhibit the assembly of polyubiquitin. On the other hand, the UbL domain interacts with the poly-Ub binding site 2 (PUbS2) domain of the S5a protein, which can carry polyubiquitinated substrates into the proteasome. We calculated the NMR structure of the UbL domain of hHR23B and determined binding surfaces of UbL and Ub to UBA1, UBA2, of hHR23B and PUbS2 of S5a by using chemical shift perturbation. Interestingly, the surfaces of UbL and Ub that bind to UBA1, UBA2, and PUbS2 are similar, consisting of five beta-strands and their connecting loops. This is the first report that an intramolecular interaction between UbL and UBA domains is possible, and this interaction could be important for the control of proteolysis by hHR23B. The binding specificities of UbL and Ub for PUbS1, PUbS2, and general ubiquitin-interacting motifs, which share the LALA motif, were evaluated. The UBA domains bind to the surface of Ub including Lys-48, which is required for multiubiquitin assembly, possibly explaining the observed inhibition of multiubiquitination by hHR23B. The UBA domains bind to UbL through electrostatic interactions supported by hydrophobic interactions and to Ub mainly through hydrophobic interactions supported by electrostatic interactions.

Selected figure(s)

Figure 1.
FIG. 1. Structure of the UbL domain in hHR23B derived from NMR experiments. Left, the 14 calculated structures were superimposed as a stereo view. Right, the ribbon diagram of one selected structure obtained with the MOLMOL program shows five -strands, one long -helix and one turn of -helix, and one short 3[10] helix.

Figure 3.
FIG. 3. Surface potential maps and surface mapping of chemical shift perturbations. Electrostatic potential maps were overlaid on the molecular surface of all domains of hHR23B and Ub with a cutoff value of 10 kT/e. The molecules of (i) UbL and Ub and (ii) UBA1 and UBA2 were matched to have the same surfaces, respectively. The amount of chemical shift perturbation was represented by using the following different colors: violet red, red, orange red, orange, and yellow, respectively, from high to low perturbation residues. The boxed figure is the model structure of -helical region of PUbS2 from S5a.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 36621-36627) copyright 2003.

Figures were selected by an automated process.