PDBsum entry 3h7p

Signaling protein

PDB id: 3h7p

Contents

Protein chains

75 a.a. *

76 a.a. *

Metals

_CD ×7

Waters ×107

* Residue conservation analysis

PDB id:

3h7p

Name:

Signaling protein

Title:

Crystal structure of k63-linked di-ubiquitin

Structure:

Ubiquitin. Chain: a. Engineered: yes. Mutation: yes. Ubiquitin. Chain: b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: rps27a, uba52, uba80, ubb, ubc, ubcep1, ubcep2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.195 R-free: 0.236

Authors:

S.D.Weeks,K.C.Grasty,L.Hernandez-Cuebas,P.J.Loll

Key ref:

S.D.Weeks et al. (2009). Crystal structures of Lys-63-linked tri- and di-ubiquitin reveal a highly extended chain architecture. Proteins, 77, 753-759. PubMed id: 19731378 DOI: 10.1002/prot.22568

Date:

28-Apr-09 Release date: 22-Sep-09

Protein chain

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 75 a.a.*

Protein chain

P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens

Seq: 685 a.a.

Struc: 76 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1002/prot.22568

Proteins 77:753-759 (2009)

PubMed id: 19731378

Crystal structures of Lys-63-linked tri- and di-ubiquitin reveal a highly extended chain architecture.

S.D.Weeks, K.C.Grasty, L.Hernandez-Cuebas, P.J.Loll.

ABSTRACT

The covalent attachment of different types of poly-ubiquitin chains signal different outcomes for the proteins so targeted. For example, a protein modified with Lys-48-linked poly-ubiquitin chains is targeted for proteasomal degradation, whereas Lys-63-linked chains encode nondegradative signals. The structural features that enable these different types of chains to encode different signals have not yet been fully elucidated. We report here the X-ray crystal structures of Lys-63-linked tri- and di-ubiquitin at resolutions of 2.3 and 1.9 A, respectively. The tri- and di-ubiquitin species adopt essentially identical structures. In both instances, the ubiquitin chain assumes a highly extended conformation with a left-handed helical twist; the helical chain contains four ubiquitin monomers per turn and has a repeat length of approximately 110 A. Interestingly, Lys-48 ubiquitin chains also adopt a left-handed helical structure with a similar repeat length. However, the Lys-63 architecture is much more open than that of Lys-48 chains and exposes much more of the ubiquitin surface for potential recognition events. These new crystal structures are consistent with the results of solution studies of Lys-63 chain conformation, and reveal the structural basis for differential recognition of Lys-63 versus Lys-48 chains.

Selected figure(s)

Figure 1.
Figure 1. (a) Verification of the ubiquitin species contained within our crystals. Lane 1, purified tri-ubiquitin; Lane 2, purified di-ubiquitin; Lanes 3 and 4, molecular weight markers (molecular weights are shown in the space between the two gels); Lane 5, a different sample of purified di-ubiquitin that was used for crystallization experiments; Lane 6, washed and dissolved di-ubiquitin crystals; Lane 7, washed and dissolved tri-ubiquitin crystals. Crystals were washed repeatedly with protein-free mother liquor, transferred to sample buffer and run on a 12-20% SDS-PAGE gradient gel, which was fixed and stained with Coomassie Brilliant Blue. The formation of SDS-resistant higher molecular weight species is likely due to residual PEG in the dissolved crystals. (b) Structure of the di-ubiquitin chain found in the asymmetric unit of both the di- and tri-ubiquitin crystals. The distal molecule is colored cyan and the proximal molecule yellow. The side chains of Lys-63 (on the proximal molecule) and Arg-63 (on the distal molecule) are shown in ball-and-stick representation. (c) Positional disorder in the tri-ubiquitin structure. At top is shown a portion of one of the extended ubiquitin chains running throughout the crystal; the distal and proximal ends of the chain are marked. Three adjacent asymmetric units are shown (A -B , A-B, and A -B ), separated by dotted lines. Below is a schematic representation of the packing of the tri-ubiquitin species. The distal-most subunit of the trimer will alternately occupy the A and B positions in the asymmetric unit. Figures 1 and 2 were prepared using MacPyMol (http://www.pymol.org).

Figure 2.
Figure 2. Stereo views of K63- and K48-linked ubiquitin chains. Upper panel: The extended K63-linked ubiquitin chain that runs through the di- and tri-ubiquitin crystals. Shown are surface representations for six monomers (three adjacent asymmetric units). Molecules occupying the distal position are colored blue and molecules in the proximal position are colored yellow. The proximal end of the chain is at the bottom of the figure, and the distal end at the top. On each molecule, the hydrophobic patch comprising residues Leu-8, Ile-44, and Val-70 is colored red. Lower panel: A tetramer of K48-linked ubiquitin molecules. Starting from the distal end and moving toward the proximal end of the chain, the monomers are colored cyan, magenta, blue, and yellow, respectively. The hydrophobic patch on each monomer is colored red, as in the upper panel.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2009, 77, 753-759) copyright 2009.