spacer
spacer

PDBsum entry 1u9a

Go to PDB code: 
protein links
Ubiquitin-conjugating enzyme PDB id
1u9a
Jmol
Contents
Protein chain
160 a.a. *
Waters ×103
* Residue conservation analysis
PDB id:
1u9a
Name: Ubiquitin-conjugating enzyme
Title: Human ubiquitin-conjugating enzyme ubc9
Structure: Ubiquitin-conjugating enzyme. Chain: a. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.160     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:
11-Feb-97     Release date:   15-May-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P63280  (UBC9_MOUSE) -  SUMO-conjugating enzyme UBC9
Seq:
Struc:
158 a.a.
160 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     synapse   8 terms 
  Biological process     viral reproduction   15 terms 
  Biochemical function     nucleotide binding     14 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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21139563 M.Grünwald, and F.Bono (2011).
Structure of Importin13-Ubc9 complex: nuclear import and release of a key regulator of sumoylation.
  EMBO J, 30, 427-438.
PDB code: 2xwu
21209884 J.Wang, A.M.Taherbhoy, H.W.Hunt, S.N.Seyedin, D.W.Miller, D.J.Miller, D.T.Huang, and B.A.Schulman (2010).
Crystal structure of UBA2(ufd)-Ubc9: insights into E1-E2 interactions in Sumo pathways.
  PLoS One, 5, e15805.
PDB codes: 3ong 3onh
19352404 B.A.Schulman, and J.W.Harper (2009).
Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways.
  Nat Rev Mol Cell Biol, 10, 319-331.  
19452197 C.Michelle, P.Vourc'h, L.Mignon, and C.R.Andres (2009).
What was the set of ubiquitin and ubiquitin-like conjugating enzymes in the eukaryote common ancestor?
  J Mol Evol, 68, 616-628.  
18276160 A.M.Burroughs, M.Jaffee, L.M.Iyer, and L.Aravind (2008).
Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation.
  J Struct Biol, 162, 205-218.  
18691969 P.Knipscheer, A.Flotho, H.Klug, J.V.Olsen, W.J.van Dijk, A.Fish, E.S.Johnson, M.Mann, T.K.Sixma, and A.Pichler (2008).
Ubc9 sumoylation regulates SUMO target discrimination.
  Mol Cell, 31, 371-382.
PDB code: 2vrr
18492068 Z.Tang, C.M.Hecker, A.Scheschonka, and H.Betz (2008).
Protein interactions in the sumoylation cascade: lessons from X-ray structures.
  FEBS J, 275, 3003-3015.  
17466333 A.D.Capili, and C.D.Lima (2007).
Structure and analysis of a complex between SUMO and Ubc9 illustrates features of a conserved E2-Ubl interaction.
  J Mol Biol, 369, 608-618.
PDB code: 2pe6
17671979 C.Wang, O.Schueler-Furman, I.Andre, N.London, S.J.Fleishman, P.Bradley, B.Qian, and D.Baker (2007).
RosettaDock in CAPRI rounds 6-12.
  Proteins, 69, 758-763.  
17391059 F.J.Kaiser, H.J.Lüdecke, and S.Weger (2007).
SUMOylation modulates transcriptional repression by TRPS1.
  Biol Chem, 388, 381-390.  
17608723 K.Sakaguchi, A.Koshiyama, and K.Iwabata (2007).
Meiosis and small ubiquitin-related modifier (SUMO)-conjugating enzyme, Ubc9.
  FEBS J, 274, 3519-3531.  
17803212 K.Wiehe, B.Pierce, W.W.Tong, H.Hwang, J.Mintseris, and Z.Weng (2007).
The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI.
  Proteins, 69, 719-725.  
17894347 S.Chaudhury, A.Sircar, A.Sivasubramanian, M.Berrondo, and J.J.Gray (2007).
Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12.
  Proteins, 69, 793-800.  
17005699 A.Tomoiu, A.Gravel, R.M.Tanguay, and L.Flamand (2006).
Functional interaction between human herpesvirus 6 immediate-early 2 protein and ubiquitin-conjugating enzyme 9 in the absence of sumoylation.
  J Virol, 80, 10218-10228.  
16782883 R.C.van Waardenburg, D.M.Duda, C.S.Lancaster, B.A.Schulman, and M.A.Bjornsti (2006).
Distinct functional domains of Ubc9 dictate cell survival and resistance to genotoxic stress.
  Mol Cell Biol, 26, 4958-4969.
PDB code: 2gjd
15694336 D.T.Huang, A.Paydar, M.Zhuang, M.B.Waddell, J.M.Holton, and B.A.Schulman (2005).
Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1.
  Mol Cell, 17, 341-350.
PDB code: 1y8x
16224784 H.Ding, Y.Yang, J.Zhang, J.Wu, H.Liu, and Y.Shi (2005).
Structural basis for SUMO-E2 interaction revealed by a complex model using docking approach in combination with NMR data.
  Proteins, 61, 1050-1058.
PDB code: 1z5q
16211493 K.Saxena, D.M.Jacobs, M.Vogtherr, S.Grimme, B.Elshort, B.Pescatore, M.Betz, U.Schieborr, T.Langer, H.Schwalbe, and K.Fiebig (2005).
Backbone NMR assignment of the human E2 ubiquitin conjugating enzyme UbcH5alpha (F72K,F82S) double mutant.
  J Biomol NMR, 32, 338.  
15608651 M.H.Tatham, S.Kim, E.Jaffray, J.Song, Y.Chen, and R.T.Hay (2005).
Unique binding interactions among Ubc9, SUMO and RanBP2 reveal a mechanism for SUMO paralog selection.
  Nat Struct Mol Biol, 12, 67-74.  
16300471 Y.Y.Mo, and S.J.Moschos (2005).
Targeting Ubc9 for cancer therapy.
  Expert Opin Ther Targets, 9, 1203-1216.  
15378033 A.Pichler, P.Knipscheer, H.Saitoh, T.K.Sixma, and F.Melchior (2004).
The RanBP2 SUMO E3 ligase is neither HECT- nor RING-type.
  Nat Struct Mol Biol, 11, 984-991.  
15062086 C.Dominguez, A.M.Bonvin, G.S.Winkler, F.M.van Schaik, H.T.Timmers, and R.Boelens (2004).
Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches.
  Structure, 12, 633-644.
PDB code: 1ur6
15189146 E.S.Johnson (2004).
Protein modification by SUMO.
  Annu Rev Biochem, 73, 355-382.  
15273307 N.Nameki, M.Yoneyama, S.Koshiba, N.Tochio, M.Inoue, E.Seki, T.Matsuda, Y.Tomo, T.Harada, K.Saito, N.Kobayashi, T.Yabuki, M.Aoki, E.Nunokawa, N.Matsuda, N.Sakagami, T.Terada, M.Shirouzu, M.Yoshida, H.Hirota, T.Osanai, A.Tanaka, T.Arakawa, P.Carninci, J.Kawai, Y.Hayashizaki, K.Kinoshita, P.Güntert, T.Kigawa, and S.Yokoyama (2004).
Solution structure of the RWD domain of the mouse GCN2 protein.
  Protein Sci, 13, 2089-2100.
PDB code: 1ukx
15341722 P.J.Winn, T.L.Religa, J.N.Battey, A.Banerjee, and R.C.Wade (2004).
Determinants of functionality in the ubiquitin conjugating enzyme family.
  Structure, 12, 1563-1574.  
14579323 L.N.Kinch, Y.Qi, T.J.Hubbard, and N.V.Grishin (2003).
CASP5 target classification.
  Proteins, 53, 340-351.  
14517261 P.Y.Wu, M.Hanlon, M.Eddins, C.Tsui, R.S.Rogers, J.P.Jensen, M.J.Matunis, A.M.Weissman, A.M.Weisman, A.M.Weissman, C.Wolberger, C.P.Wolberger, and C.M.Pickart (2003).
A conserved catalytic residue in the ubiquitin-conjugating enzyme family.
  EMBO J, 22, 5241-5250.  
14531806 S.M.Gisler, S.Pribanic, D.Bacic, P.Forrer, A.Gantenbein, L.A.Sabourin, A.Tsuji, Z.S.Zhao, E.Manser, J.Biber, and H.Murer (2003).
PDZK1: I. a major scaffolder in brush borders of proximal tubular cells.
  Kidney Int, 64, 1733-1745.  
12005425 A.P.VanDemark, and C.P.Hill (2002).
SUMO wrestling with specificity.
  Structure, 10, 281-282.  
  11806825 D.Jones, E.Crowe, T.A.Stevens, and E.P.Candido (2002).
Functional and phylogenetic analysis of the ubiquitylation system in Caenorhabditis elegans: ubiquitin-conjugating enzymes, ubiquitin-activating enzymes, and ubiquitin-like proteins.
  Genome Biol, 3, RESEARCH0002.  
12006492 O.Pornillos, S.L.Alam, R.L.Rich, D.G.Myszka, D.R.Davis, and W.I.Sundquist (2002).
Structure and functional interactions of the Tsg101 UEV domain.
  EMBO J, 21, 2397-2406.
PDB codes: 1kpp 1kpq
11331779 A.L.Kurtzman, and N.Schechter (2001).
Ubc9 interacts with a nuclear localization signal and mediates nuclear localization of the paired-like homeobox protein Vsx-1 independent of SUMO-1 modification.
  Proc Natl Acad Sci U S A, 98, 5602-5607.  
11395416 C.M.Pickart (2001).
Mechanisms underlying ubiquitination.
  Annu Rev Biochem, 70, 503-533.  
11533242 C.Ptak, C.Gwozd, J.T.Huzil, T.J.Gwozd, G.Garen, and M.J.Ellison (2001).
Creation of a pluripotent ubiquitin-conjugating enzyme.
  Mol Cell Biol, 21, 6537-6548.  
11255249 D.Sleep, C.Finnis, A.Turner, and L.Evans (2001).
Yeast 2 microm plasmid copy number is elevated by a mutation in the nuclear gene UBC4.
  Yeast, 18, 403-421.  
11031248 F.Melchior (2000).
SUMO--nonclassical ubiquitin.
  Annu Rev Cell Dev Biol, 16, 591-626.  
10350465 F.Jiang, and R.Basavappa (1999).
Crystal structure of the cyclin-specific ubiquitin-conjugating enzyme from clam, E2-C, at 2.0 A resolution.
  Biochemistry, 38, 6471-6478.
PDB code: 2e2c
9931006 Q.Liu, Y.C.Yuan, B.Shen, D.J.Chen, and Y.Chen (1999).
Conformational flexibility of a ubiquitin conjugation enzyme (E2).
  Biochemistry, 38, 1415-1425.  
10377438 S.R.Chakrabarti, R.Sood, S.Ganguly, S.Bohlander, Z.Shen, and G.Nucifora (1999).
Modulation of TEL transcription activity by interaction with the ubiquitin-conjugating enzyme UBC9.
  Proc Natl Acad Sci U S A, 96, 7467-7472.  
10077596 S.Y.Cai, R.W.Babbitt, and V.T.Marchesi (1999).
A mutant deubiquitinating enzyme (Ubp-M) associates with mitotic chromosomes and blocks cell division.
  Proc Natl Acad Sci U S A, 96, 2828-2833.  
9759494 A.Hershko, and A.Ciechanover (1998).
The ubiquitin system.
  Annu Rev Biochem, 67, 425-479.  
9657692 L.D.Mastrandrea, E.M.Kasperek, E.G.Niles, and C.M.Pickart (1998).
Core domain mutation (S86Y) selectively inactivates polyubiquitin chain synthesis catalyzed by E2-25K.
  Biochemistry, 37, 9784-9792.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.