PDBsum entry: 1u9b

Ligase

PDB id: 1u9b

Contents

Protein chain

159 a.a. *

Waters ×96

* Residue conservation analysis

PDB id:

1u9b

Name:

Ligase

Title:

Murine/human ubiquitin-conjugating enzyme ubc9

Structure:

Ubiquitin-conjugating enzyme e9. Chain: a. Synonym: ubc9. Engineered: yes. Mutation: yes. Other_details: mammalian

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.185 R-free: 0.250

Authors:

H.Tong,G.Hateboer,A.Perrakis,R.Bernards,T.K.Sixma

Key ref:

H.Tong et al. (1997). Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system. J Biol Chem, 272, 21381-21387. PubMed id: 9261152 DOI: 10.1074/jbc.272.34.21381

Date:

20-May-97 Release date: 07-Jul-97

Protein chain

P63280  (UBC9_MOUSE) -  SUMO-conjugating enzyme UBC9

Seq: 158 a.a.

Struc: 159 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: synapse (6 terms)
• Biological process: cell cycle (15 terms)
• Biochemical function: nucleotide binding (10 terms)

DOI no: 10.1074/jbc.272.34.21381

J Biol Chem 272:21381-21387 (1997)

PubMed id: 9261152

Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system.

H.Tong, G.Hateboer, A.Perrakis, R.Bernards, T.K.Sixma.

ABSTRACT

Murine/human ubiquitin-conjugating enzyme Ubc9 is a functional homolog of Saccharomyces cerevisiae Ubc9 that is essential for the viability of yeast cells with a specific role in the G2-M transition of the cell cycle. The structure of recombinant mammalian Ubc9 has been determined from two crystal forms at 2.0 A resolution. Like Arabidopsis thaliana Ubc1 and S. cerevisiae Ubc4, murine/human Ubc9 was crystallized as a monomer, suggesting that previously reported hetero- and homo-interactions among Ubcs may be relatively weak or indirect. Compared with the known crystal structures of Ubc1 and Ubc4, which regulate different cellular processes, Ubc9 has a 5-residue insertion that forms a very exposed tight beta-hairpin and a 2-residue insertion that forms a bulge in a loop close to the active site. Mammalian Ubc9 also possesses a distinct electrostatic potential distribution that may provide possible clues to its remarkable ability to interact with other proteins. The 2-residue insertion and other sequence and structural heterogeneity observed at the catalytic site suggest that different Ubcs may utilize catalytic mechanisms of varying efficiency and substrate specificity.

Selected figure(s)

Figure 1.
Fig. 1. Schematic representation of the Ubc9 model in the P2[1] crystal form. Helices are drawn in red and strands are drawn in green. The side chain atoms of the ubiquitin-accepting cysteine^ Cys93 are represented as yellow ball-and-sticks. The first -helix (residues 1-18) and the four -strands (residues 25-30, 36-46, 57-63, and 74-77) consist of amino acids from the N-terminal half^ of the molecule, whereas the three other -helices (residues 109-121, 131-139, and 141-154) consist of residues from the C-terminal half. These secondary structure elements comprise approximately 50% of the structure (17% -strands and 33% -helices). This figure^ was prepared using MOLSCRIPT (55).

Figure 5.
Fig. 5. Electrostatic potentials mapped onto the surface of the mammalian Ubc9, Arabidopsis Ubc1, and S. cerevisiae Ubc4 structures. Among the four different orientations, the "right" view corresponds to the active site cysteine on the right-hand side of the figure. This view is similar to that of Fig. 3A. The rest are generated^ by successive rotations of 90° around the vertical axis. The color spectrum from red to blue corresponds to changes from negative^ to positive potential ( 10 to 10 K[B]T, where K[B] is the Boltzmann constant). This diagram was produced using GRASP (50).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (1997, 272, 21381-21387) copyright 1997.

Figures were selected by the author.