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PDBsum entry 1z5s

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protein Protein-protein interface(s) links
Ligase PDB id
1z5s
Jmol
Contents
Protein chains
156 a.a. *
78 a.a. *
156 a.a. *
65 a.a. *
Waters ×28
* Residue conservation analysis
PDB id:
1z5s
Name: Ligase
Title: Crystal structure of a complex between ubc9, sumo-1, rangap1 and nup358/ranbp2
Structure: Ubiquitin-conjugating enzyme e2 i. Chain: a. Synonym: ubiquitin-protein ligase i, ubiquitin carrier protein i, sumo-1-protein ligase, sumo- 1 conjugating enzyme, ubiquitin carrier protein 9, p18. Engineered: yes. Ubiquitin-like protein smt3c. Chain: b. Synonym: ubiquitin-homology domain protein pic1, ubiquitin-
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ube2i, ubc9, ubce9. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: ubl1, smt3c, smt3h3. Gene: rangap1. Gene: ranbp2, nup358.
Biol. unit: Tetramer (from PQS)
Resolution:
3.01Å     R-factor:   0.247     R-free:   0.290
Authors: D.Reverter,C.D.Lima
Key ref:
D.Reverter and C.D.Lima (2005). Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex. Nature, 435, 687-692. PubMed id: 15931224 DOI: 10.1038/nature03588
Date:
19-Mar-05     Release date:   07-Jun-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P63279  (UBC9_HUMAN) -  SUMO-conjugating enzyme UBC9
Seq:
Struc:
158 a.a.
156 a.a.
Protein chain
Pfam   ArchSchema ?
P63165  (SUMO1_HUMAN) -  Small ubiquitin-related modifier 1
Seq:
Struc:
101 a.a.
78 a.a.
Protein chain
Pfam   ArchSchema ?
P46060  (RAGP1_HUMAN) -  Ran GTPase-activating protein 1
Seq:
Struc:
 
Seq:
Struc:
587 a.a.
156 a.a.
Protein chain
Pfam   ArchSchema ?
P49792  (RBP2_HUMAN) -  E3 SUMO-protein ligase RanBP2
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
3224 a.a.
65 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     synapse   9 terms 
  Biological process     viral reproduction   18 terms 
  Biochemical function     nucleotide binding     15 terms  

 

 
DOI no: 10.1038/nature03588 Nature 435:687-692 (2005)
PubMed id: 15931224  
 
 
Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex.
D.Reverter, C.D.Lima.
 
  ABSTRACT  
 
SUMO-1 (for small ubiquitin-related modifier) belongs to the ubiquitin (Ub) and ubiquitin-like (Ubl) protein family. SUMO conjugation occurs on specific lysine residues within protein targets, regulating pathways involved in differentiation, apoptosis, the cell cycle and responses to stress by altering protein function through changes in activity or cellular localization or by protecting substrates from ubiquitination. Ub/Ubl conjugation occurs in sequential steps and requires the concerted action of E2 conjugating proteins and E3 ligases. In addition to being a SUMO E3, the nucleoporin Nup358/RanBP2 localizes SUMO-conjugated RanGAP1 to the cytoplasmic face of the nuclear pore complex by means of interactions in a complex that also includes Ubc9, the SUMO E2 conjugating protein. Here we describe the 3.0-A crystal structure of a four-protein complex of Ubc9, a Nup358/RanBP2 E3 ligase domain (IR1-M) and SUMO-1 conjugated to the carboxy-terminal domain of RanGAP1. Structural insights, combined with biochemical and kinetic data obtained with additional substrates, support a model in which Nup358/RanBP2 acts as an E3 by binding both SUMO and Ubc9 to position the SUMO-E2-thioester in an optimal orientation to enhance conjugation.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Structure of SUMO -RanGAP1 -Ubc9 -Nup358/RanBP2 complex. a, Ribbon and transparent-surface representation for the complex between SUMO-1 (yellow), Ubc9 (blue), RanGAP1 (pink) and Nup358/RanBP2 (magenta). Each protein is labelled. The SUMO C-terminal glycine (Gly 97) and RanGAP1 Lys 524 are represented by solid bonds located near the image centre. b, Orthogonal view of the complex. c, Orthogonal view of the complex to highlight the extended Nup358/RanBP2 structure. The N and C termini of Nup358/RanBP2 are indicated. Structural graphics were generated with Pymol (http://pymol.sourceforge.net).
Figure 2.
Figure 2: E2 active site in complex with RanGAP1 -SUMO-1. Stereo view of the E2 active site in complex with SUMO-1 -RanGAP1 in ribbon and solid-bond representation. Residues are labelled, and hydrogen-bonding interactions are indicated by dashed lines. SUMO-1, RanGAP1 and Ubc9 are coloured yellow, pink and blue as in Fig. 1.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nature (2005, 435, 687-692) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23202584 C.Otomo, Z.Metlagel, G.Takaesu, and T.Otomo (2013).
Structure of the human ATG12~ATG5 conjugate required for LC3 lipidation in autophagy.
  Nat Struct Mol Biol, 20, 59-66.
PDB codes: 4gdk 4gdl
22382979 A.A.Armstrong, F.Mohideen, and C.D.Lima (2012).
Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2.
  Nature, 483, 59-63.
PDB codes: 3v60 3v61 3v62
22842904 A.Plechanovová, E.G.Jaffray, M.H.Tatham, J.H.Naismith, and R.T.Hay (2012).
Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis.
  Nature, 489, 115-120.
PDB code: 4ap4
22902369 H.Dou, L.Buetow, G.J.Sibbet, K.Cameron, and D.T.Huang (2012).
BIRC7-E2 ubiquitin conjugate structure reveals the mechanism of ubiquitin transfer by a RING dimer.
  Nat Struct Mol Biol, 19, 876-883.
PDB code: 4auq
21540891 C.Behrends, and J.W.Harper (2011).
Constructing and decoding unconventional ubiquitin chains.
  Nat Struct Mol Biol, 18, 520-528.  
21474068 C.C.Chang, M.T.Naik, Y.S.Huang, J.C.Jeng, P.H.Liao, H.Y.Kuo, C.C.Ho, Y.L.Hsieh, C.H.Lin, N.J.Huang, N.M.Naik, C.C.Kung, S.Y.Lin, R.H.Chen, K.S.Chang, T.H.Huang, and H.M.Shih (2011).
Structural and functional roles of Daxx SIM phosphorylation in SUMO paralog-selective binding and apoptosis modulation.
  Mol Cell, 42, 62-74.
PDB code: 2kqs
21092369 D.Barford (2011).
Structure, function and mechanism of the anaphase promoting complex (APC/C).
  Q Rev Biophys, 44, 153-190.  
21396940 I.Bosanac, L.Phu, B.Pan, I.Zilberleyb, B.Maurer, V.M.Dixit, S.G.Hymowitz, and D.S.Kirkpatrick (2011).
Modulation of K11-linkage formation by variable loop residues within UbcH5A.
  J Mol Biol, 408, 420-431.
PDB code: 3ptf
21376237 K.E.Wickliffe, S.Lorenz, D.E.Wemmer, J.Kuriyan, and M.Rape (2011).
The mechanism of linkage-specific ubiquitin chain elongation by a single-subunit E2.
  Cell, 144, 769-781.  
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
21518904 R.N.Gilbreth, K.Truong, I.Madu, A.Koide, J.B.Wojcik, N.S.Li, J.A.Piccirilli, Y.Chen, and S.Koide (2011).
Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design.
  Proc Natl Acad Sci U S A, 108, 7751-7756.
PDB code: 3qht
20802522 T.Saether, D.R.Pattabiraman, A.H.Alm-Kristiansen, L.T.Vogt-Kielland, T.J.Gonda, and O.S.Gabrielsen (2011).
A functional SUMO-interacting motif in the transactivation domain of c-Myb regulates its myeloid transforming ability.
  Oncogene, 30, 212-222.  
21037856 C.Oberle, and C.Blattner (2010).
Regulation of the DNA Damage Response to DSBs by Post-Translational Modifications.
  Curr Genomics, 11, 184-198.  
20571586 C.Strambio-De-Castillia, M.Niepel, and M.P.Rout (2010).
The nuclear pore complex: bridging nuclear transport and gene regulation.
  Nat Rev Mol Cell Biol, 11, 490-501.  
21158740 D.M.Wenzel, K.E.Stoll, and R.E.Klevit (2010).
E2s: structurally economical and functionally replete.
  Biochem J, 433, 31-42.  
20152160 E.Sakata, T.Satoh, S.Yamamoto, Y.Yamaguchi, M.Yagi-Utsumi, E.Kurimoto, K.Tanaka, S.Wakatsuki, and K.Kato (2010).
Crystal structure of UbcH5b~ubiquitin intermediate: insight into the formation of the self-assembled E2~Ub conjugates.
  Structure, 18, 138-147.
PDB code: 3a33
20396627 G.Brahemi, A.M.Burger, A.D.Westwell, and A.Brancale (2010).
Homology Modelling of Human E1 Ubiquitin Activating Enzyme.
  Lett Drug Des Discov, 7, 57-62.  
21102611 J.R.Gareau, and C.D.Lima (2010).
The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition.
  Nat Rev Mol Cell Biol, 11, 861-871.  
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
20462400 K.A.Wilkinson, and J.M.Henley (2010).
Mechanisms, regulation and consequences of protein SUMOylation.
  Biochem J, 428, 133-145.  
20347421 K.Wu, J.Kovacev, and Z.Q.Pan (2010).
Priming and extending: a UbcH5/Cdc34 E2 handoff mechanism for polyubiquitination on a SCF substrate.
  Mol Cell, 37, 784-796.  
  20865051 M.Tozluo─člu, E.Karaca, R.Nussinov, and T.Halilo─člu (2010).
A mechanistic view of the role of E3 in sumoylation.
  PLoS Comput Biol, 6, 0.  
20590526 N.Kolli, J.Mikolajczyk, M.Drag, D.Mukhopadhyay, N.Moffatt, M.Dasso, G.Salvesen, and K.D.Wilkinson (2010).
Distribution and paralogue specificity of mammalian deSUMOylating enzymes.
  Biochem J, 430, 335-344.  
20941751 N.Tanaka, M.Goto, A.Kawasaki, T.Sasano, K.Eto, R.Nishi, K.Sugasawa, S.Abe, and H.Saitoh (2010).
An EF-hands protein, centrin-1, is an EGTA-sensitive SUMO-interacting protein in mouse testis.
  Cell Biochem Funct, 28, 604-612.  
20176810 S.H.Yang, and A.D.Sharrocks (2010).
The SUMO E3 ligase activity of Pc2 is coordinated through a SUMO interaction motif.
  Mol Cell Biol, 30, 2193-2205.  
20164921 S.K.Olsen, A.D.Capili, X.Lu, D.S.Tan, and C.D.Lima (2010).
Active site remodelling accompanies thioester bond formation in the SUMO E1.
  Nature, 463, 906-912.
PDB codes: 3kyc 3kyd
20196770 X.Li, S.Vadrevu, A.Dunlop, J.Day, N.Advant, J.Troeger, E.Klussmann, E.Jaffrey, R.T.Hay, D.R.Adams, M.D.Houslay, and G.S.Baillie (2010).
Selective SUMO modification of cAMP-specific phosphodiesterase-4D5 (PDE4D5) regulates the functional consequences of phosphorylation by PKA and ERK.
  Biochem J, 428, 55-65.  
19107417 A.A.Yunus, and C.D.Lima (2009).
Purification of SUMO conjugating enzymes and kinetic analysis of substrate conjugation.
  Methods Mol Biol, 497, 167-186.  
19748360 A.A.Yunus, and C.D.Lima (2009).
Structure of the Siz/PIAS SUMO E3 ligase Siz1 and determinants required for SUMO modification of PCNA.
  Mol Cell, 35, 669-682.
PDB code: 3i2d
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.  
19684601 F.Mohideen, A.D.Capili, P.M.Bilimoria, T.Yamada, A.Bonni, and C.D.Lima (2009).
A molecular basis for phosphorylation-dependent SUMO conjugation by the E2 UBC9.
  Nat Struct Mol Biol, 16, 945-952.  
19308990 G.A.Spoden, D.Morandell, D.Ehehalt, M.Fiedler, P.Jansen-Dürr, M.Hermann, and W.Zwerschke (2009).
The SUMO-E3 ligase PIAS3 targets pyruvate kinase M2.
  J Cell Biochem, 107, 293-302.  
20064473 H.B.Kamadurai, J.Souphron, D.C.Scott, D.M.Duda, D.J.Miller, D.Stringer, R.C.Piper, and B.A.Schulman (2009).
Insights into ubiquitin transfer cascades from a structure of a UbcH5B approximately ubiquitin-HECT(NEDD4L) complex.
  Mol Cell, 36, 1095-1102.
PDB codes: 3jvz 3jw0
19394292 J.Ouyang, Y.Shi, A.Valin, Y.Xuan, and G.Gill (2009).
Direct binding of CoREST1 to SUMO-2/3 contributes to gene-specific repression by the LSD1/CoREST1/HDAC complex.
  Mol Cell, 34, 145-154.  
19785004 J.Song, J.Wang, A.A.Jozwiak, W.Hu, P.M.Swiderski, and Y.Chen (2009).
Stability of thioester intermediates in ubiquitin-like modifications.
  Protein Sci, 18, 2492-2499.  
19107413 M.B.Kroetz, and M.Hochstrasser (2009).
Identification of SUMO-interacting proteins by yeast two-hybrid analysis.
  Methods Mol Biol, 497, 107-120.  
19874575 M.E.Matyskiela, M.C.Rodrigo-Brenni, and D.O.Morgan (2009).
Mechanisms of ubiquitin transfer by the anaphase-promoting complex.
  J Biol, 8, 92.  
19325621 M.Hochstrasser (2009).
Origin and function of ubiquitin-like proteins.
  Nature, 458, 422-429.  
19526197 M.M.Rytinki, S.Kaikkonen, P.Pehkonen, T.Jääskeläinen, and J.J.Palvimo (2009).
PIAS proteins: pleiotropic interactors associated with SUMO.
  Cell Mol Life Sci, 66, 3029-3041.  
19560420 R.Das, J.Mariano, Y.C.Tsai, R.C.Kalathur, Z.Kostova, J.Li, S.G.Tarasov, R.L.McFeeters, A.S.Altieri, X.Ji, R.A.Byrd, and A.M.Weissman (2009).
Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78.
  Mol Cell, 34, 674-685.
PDB code: 3h8k
19489725 R.J.Deshaies, and C.A.Joazeiro (2009).
RING domain E3 ubiquitin ligases.
  Annu Rev Biochem, 78, 399-434.  
19497852 S.Mukherjee, M.Thomas, N.Dadgar, A.P.Lieberman, and J.A.Iñiguez-Lluhí (2009).
Small ubiquitin-like modifier (SUMO) modification of the androgen receptor attenuates polyglutamine-mediated aggregation.
  J Biol Chem, 284, 21296-21306.  
19285941 S.Zhu, J.Goeres, K.M.Sixt, M.Békés, X.D.Zhang, G.S.Salvesen, and M.J.Matunis (2009).
Protection from isopeptidase-mediated deconjugation regulates paralog-selective sumoylation of RanGAP1.
  Mol Cell, 33, 570-580.  
19923268 Y.Wang, and M.Dasso (2009).
SUMOylation and deSUMOylation at a glance.
  J Cell Sci, 122, 4249-4252.  
19139279 Z.Wang, and G.Prelich (2009).
Quality control of a transcriptional regulator by SUMO-targeted degradation.
  Mol Cell Biol, 29, 1694-1706.  
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.  
18313922 B.Palancade, and V.Doye (2008).
Sumoylating and desumoylating enzymes at nuclear pores: underpinning their unexpected duties?
  Trends Cell Biol, 18, 174-183.  
18273061 C.Ng, R.A.Jackson, J.P.Buschdorf, Q.Sun, G.R.Guy, and J.Sivaraman (2008).
Structural basis for a novel intrapeptidyl H-bond and reverse binding of c-Cbl-TKB domain substrates.
  EMBO J, 27, 804-816.
PDB codes: 3bum 3bun 3buo 3buw 3bux
18264111 D.T.Huang, M.Zhuang, O.Ayrault, and B.A.Schulman (2008).
Identification of conjugation specificity determinants unmasks vestigial preference for ubiquitin within the NEDD8 E2.
  Nat Struct Mol Biol, 15, 280-287.  
18538649 F.Mohideen, and C.D.Lima (2008).
SUMO takes control of a ubiquitin-specific protease.
  Mol Cell, 30, 539-540.  
18302266 H.Chen, P.Boontheung, R.R.Loo, Y.Xie, J.A.Loo, J.Y.Rao, and M.D.Collins (2008).
Proteomic analysis to characterize differential mouse strain sensitivity to cadmium-induced forelimb teratogenesis.
  Birth Defects Res A Clin Mol Teratol, 82, 187-199.  
18155241 H.Windecker, and H.D.Ulrich (2008).
Architecture and assembly of poly-SUMO chains on PCNA in Saccharomyces cerevisiae.
  J Mol Biol, 376, 221-231.  
18403209 J.J.Perry, J.A.Tainer, and M.N.Boddy (2008).
A SIM-ultaneous role for SUMO and ubiquitin.
  Trends Biochem Sci, 33, 201-208.  
18701921 J.L.Parker, A.Bucceri, A.A.Davies, K.Heidrich, H.Windecker, and H.D.Ulrich (2008).
SUMO modification of PCNA is controlled by DNA.
  EMBO J, 27, 2422-2431.  
18708356 J.Zhu, S.Zhu, C.M.Guzzo, N.A.Ellis, K.S.Sung, C.Y.Choi, and M.J.Matunis (2008).
Small ubiquitin-related modifier (SUMO) binding determines substrate recognition and paralog-selective SUMO modification.
  J Biol Chem, 283, 29405-29415.  
18344540 K.Schwamborn, P.Knipscheer, E.van Dijk, W.J.van Dijk, T.K.Sixma, R.H.Meloen, and J.P.Langedijk (2008).
SUMO assay with peptide arrays on solid support: insights into SUMO target sites.
  J Biochem, 144, 39-49.  
18838537 L.A.Campbell, E.J.Faivre, M.D.Show, J.G.Ingraham, J.Flinders, J.D.Gross, and H.A.Ingraham (2008).
Decreased recognition of SUMO-sensitive target genes following modification of SF-1 (NR5A1).
  Mol Cell Biol, 28, 7476-7486.  
18485873 L.Jin, A.Williamson, S.Banerjee, I.Philipp, and M.Rape (2008).
Mechanism of ubiquitin-chain formation by the human anaphase-promoting complex.
  Cell, 133, 653-665.  
18025037 M.A.Park, Y.J.Seok, G.Jeong, and J.S.Lee (2008).
SUMO1 negatively regulates BRCA1-mediated transcription, via modulation of promoter occupancy.
  Nucleic Acids Res, 36, 263-283.  
18218095 M.Dasso (2008).
Emerging roles of the SUMO pathway in mitosis.
  Cell Div, 3, 5.  
18394551 M.S.Navarro, and J.Bachant (2008).
RanBP2: a tumor suppressor with a new twist on TopoII, SUMO, and centromeres.
  Cancer Cell, 13, 293-295.  
18439914 M.Shitashige, R.Satow, K.Honda, M.Ono, S.Hirohashi, and T.Yamada (2008).
Regulation of Wnt signaling by the nuclear pore complex.
  Gastroenterology, 134, 1961.  
17377839 M.V.Karamouzis, P.A.Konstantinopoulos, F.A.Badra, and A.G.Papavassiliou (2008).
SUMO and estrogen receptors in breast cancer.
  Breast Cancer Res Treat, 107, 195-210.  
18842587 N.Sekiyama, T.Ikegami, T.Yamane, M.Ikeguchi, Y.Uchimura, D.Baba, M.Ariyoshi, H.Tochio, H.Saitoh, and M.Shirakawa (2008).
Structure of the Small Ubiquitin-like Modifier (SUMO)-interacting Motif of MBD1-containing Chromatin-associated Factor 1 Bound to SUMO-3.
  J Biol Chem, 283, 35966-35975.  
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
18359863 S.F.Martin, M.H.Tatham, R.T.Hay, and I.D.Samuel (2008).
Quantitative analysis of multi-protein interactions using FRET: application to the SUMO pathway.
  Protein Sci, 17, 777-784.  
18845677 S.Otsuka, S.Iwasaka, Y.Yoneda, K.Takeyasu, and S.H.Yoshimura (2008).
Individual binding pockets of importin-beta for FG-nucleoporins have different binding properties and different sensitivities to RanGTP.
  Proc Natl Acad Sci U S A, 105, 16101-16106.  
18562626 S.R.Holmstrom, S.Chupreta, A.Y.So, and J.A.Iñiguez-Lluhí (2008).
SUMO-mediated inhibition of glucocorticoid receptor synergistic activity depends on stable assembly at the promoter but not on DAXX.
  Mol Endocrinol, 22, 2061-2075.  
18281463 V.Vethantham, N.Rao, and J.L.Manley (2008).
Sumoylation regulates multiple aspects of mammalian poly(A) polymerase function.
  Genes Dev, 22, 499-511.  
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.  
17956732 A.Carbia-Nagashima, J.Gerez, C.Perez-Castro, M.Paez-Pereda, S.Silberstein, G.K.Stalla, F.Holsboer, and E.Arzt (2007).
RSUME, a small RWD-containing protein, enhances SUMO conjugation and stabilizes HIF-1alpha during hypoxia.
  Cell, 131, 309-323.  
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
17919899 A.D.Capili, and C.D.Lima (2007).
Taking it step by step: mechanistic insights from structural studies of ubiquitin/ubiquitin-like protein modification pathways.
  Curr Opin Struct Biol, 17, 726-735.  
17803214 A.Heifetz, S.Pal, and G.R.Smith (2007).
Protein-protein docking: progress in CAPRI rounds 6-12 using a combination of methods: the introduction of steered solvated molecular dynamics.
  Proteins, 69, 816-822.  
17477837 B.T.Dye, and B.A.Schulman (2007).
Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins.
  Annu Rev Biophys Biomol Struct, 36, 131-150.  
17475278 D.M.Duda, R.C.van Waardenburg, L.A.Borg, S.McGarity, A.Nourse, M.B.Waddell, M.A.Bjornsti, and B.A.Schulman (2007).
Structure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: conservation of a non-covalent ubiquitin-like protein-E2 complex as a platform for selective interactions within a SUMO pathway.
  J Mol Biol, 369, 619-630.
PDB code: 2eke
17220875 D.T.Huang, H.W.Hunt, M.Zhuang, M.D.Ohi, J.M.Holton, and B.A.Schulman (2007).
Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity.
  Nature, 445, 394-398.
PDB code: 2nvu
17762864 H.Sun, J.D.Leverson, and T.Hunter (2007).
Conserved function of RNF4 family proteins in eukaryotes: targeting a ubiquitin ligase to SUMOylated proteins.
  EMBO J, 26, 4102-4112.  
17586545 H.X.Zhou, and S.Qin (2007).
Interaction-site prediction for protein complexes: a critical assessment.
  Bioinformatics, 23, 2203-2209.  
17643372 J.Wang, W.Hu, S.Cai, B.Lee, J.Song, and Y.Chen (2007).
The intrinsic affinity between E2 and the Cys domain of E1 in ubiquitin-like modifications.
  Mol Cell, 27, 228-237.
PDB code: 2px9
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.  
17545995 O.Kerscher (2007).
SUMO junction-what's your function? New insights through SUMO-interacting motifs.
  EMBO Rep, 8, 550-555.  
17933515 P.Knipscheer, and T.K.Sixma (2007).
Protein-protein interactions regulate Ubl conjugation.
  Curr Opin Struct Biol, 17, 665-673.  
18000527 R.Geiss-Friedlander, and F.Melchior (2007).
Concepts in sumoylation: a decade on.
  Nat Rev Mol Cell Biol, 8, 947-956.  
17940278 S.Chupreta, H.Brevig, L.Bai, J.L.Merchant, and J.A.Iñiguez-Lluhí (2007).
Sumoylation-dependent control of homotypic and heterotypic synergy by the Kruppel-type zinc finger protein ZBP-89.
  J Biol Chem, 282, 36155-36166.  
17803232 S.Qin, and H.X.Zhou (2007).
A holistic approach to protein docking.
  Proteins, 69, 743-749.  
17298944 X.H.Mascle, D.Germain-Desprez, P.Huynh, P.Estephan, and M.Aubry (2007).
Sumoylation of the transcriptional intermediary factor 1beta (TIF1beta), the Co-repressor of the KRAB Multifinger proteins, is required for its transcriptional activity and is modulated by the KRAB domain.
  J Biol Chem, 282, 10190-10202.  
  20103862 Y.Chen (2007).
The enzymes in ubiquitin-like post-translational modifications.
  Biosci Trends, 1, 16-25.  
17227760 Y.Yamada, N.N.Suzuki, T.Hanada, Y.Ichimura, H.Kumeta, Y.Fujioka, Y.Ohsumi, and F.Inagaki (2007).
The crystal structure of Atg3, an autophagy-related ubiquitin carrier protein (E2) enzyme that mediates Atg8 lipidation.
  J Biol Chem, 282, 8036-8043.
PDB code: 2dyt
16732283 A.A.Yunus, and C.D.Lima (2006).
Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway.
  Nat Struct Mol Biol, 13, 491-499.
PDB codes: 2grn 2gro 2grp 2grq 2grr
16475184 A.Chen, P.Y.Wang, Y.C.Yang, Y.H.Huang, J.J.Yeh, Y.H.Chou, J.T.Cheng, Y.R.Hong, and S.S.Li (2006).
SUMO regulates the cytoplasmonuclear transport of its target protein Daxx.
  J Cell Biochem, 98, 895-911.  
16567619 A.Rosendorff, S.Sakakibara, S.Lu, E.Kieff, Y.Xuan, A.DiBacco, Y.Shi, Y.Shi, and G.Gill (2006).
NXP-2 association with SUMO-2 depends on lysines required for transcriptional repression.
  Proc Natl Acad Sci U S A, 103, 5308-5313.  
16524884 C.M.Hecker, M.Rabiller, K.Haglund, P.Bayer, and I.Dikic (2006).
Specification of SUMO1- and SUMO2-interacting motifs.
  J Biol Chem, 281, 16117-16127.  
17081974 D.Branzei, J.Sollier, G.Liberi, X.Zhao, D.Maeda, M.Seki, T.Enomoto, K.Ohta, and M.Foiani (2006).
Ubc9- and mms21-mediated sumoylation counteracts recombinogenic events at damaged replication forks.
  Cell, 127, 509-522.  
16461911 D.Devos, S.Dokudovskaya, R.Williams, F.Alber, N.Eswar, B.T.Chait, M.P.Rout, and A.Sali (2006).
Simple fold composition and modular architecture of the nuclear pore complex.
  Proc Natl Acad Sci U S A, 103, 2172-2177.  
17000875 D.Mukhopadhyay, F.Ayaydin, N.Kolli, S.H.Tan, T.Anan, A.Kametaka, Y.Azuma, K.D.Wilkinson, and M.Dasso (2006).
SUSP1 antagonizes formation of highly SUMO2/3-conjugated species.
  J Cell Biol, 174, 939-949.  
17099700 D.Reverter, and C.D.Lima (2006).
Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates.
  Nat Struct Mol Biol, 13, 1060-1068.
PDB codes: 2io0 2io1 2io2 2io3
16828554 H.Remaut, and G.Waksman (2006).
Protein-protein interaction through beta-strand addition.
  Trends Biochem Sci, 31, 436-444.  
16602682 J.A.Wohlschlegel, E.S.Johnson, S.I.Reed, and J.R.Yates (2006).
Improved identification of SUMO attachment sites using C-terminal SUMO mutants and tailored protease digestion strategies.
  J Proteome Res, 5, 761-770.  
16499958 L.Penengo, M.Mapelli, A.G.Murachelli, S.Confalonieri, L.Magri, A.Musacchio, P.P.Di Fiore, S.Polo, and T.R.Schneider (2006).
Crystal structure of the ubiquitin binding domains of rabex-5 reveals two modes of interaction with ubiquitin.
  Cell, 124, 1183-1195.
PDB codes: 2c7m 2c7n
17099698 L.Shen, M.H.Tatham, C.Dong, A.Zagórska, J.H.Naismith, and R.T.Hay (2006).
SUMO protease SENP1 induces isomerization of the scissile peptide bond.
  Nat Struct Mol Biol, 13, 1069-1077.
PDB codes: 2iy0 2iy1
16857984 L.Song, S.Bhattacharya, A.A.Yunus, C.D.Lima, and C.Schindler (2006).
Stat1 and SUMO modification.
  Blood, 108, 3237-3244.  
17114057 M.D.Petroski, G.Kleiger, and R.J.Deshaies (2006).
Evaluation of a diffusion-driven mechanism for substrate ubiquitination by the SCF-Cdc34 ubiquitin ligase complex.
  Mol Cell, 24, 523-534.  
16413479 M.Hochstrasser (2006).
Lingering mysteries of ubiquitin-chain assembly.
  Cell, 124, 27-34.  
16980971 M.J.Eddins, C.M.Carlile, K.M.Gomez, C.M.Pickart, and C.Wolberger (2006).
Mms2-Ubc13 covalently bound to ubiquitin reveals the structural basis of linkage-specific polyubiquitin chain formation.
  Nat Struct Mol Biol, 13, 915-920.
PDB code: 2gmi
16319071 M.S.Macauley, W.J.Errington, M.Schärpf, C.D.Mackereth, A.G.Blaszczak, B.J.Graves, and L.P.McIntosh (2006).
Beads-on-a-string, characterization of ETS-1 sumoylated within its flexible N-terminal sequence.
  J Biol Chem, 281, 4164-4172.  
16601690 M.Wang, D.Cheng, J.Peng, and C.M.Pickart (2006).
Molecular determinants of polyubiquitin linkage selection by an HECT ubiquitin ligase.
  EMBO J, 25, 1710-1719.  
16753028 O.Kerscher, R.Felberbaum, and M.Hochstrasser (2006).
Modification of proteins by ubiquitin and ubiquitin-like proteins.
  Annu Rev Cell Dev Biol, 22, 159-180.  
16757944 P.Knipscheer, and T.K.Sixma (2006).
Divide and conquer: the E2 active site.
  Nat Struct Mol Biol, 13, 474-476.  
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
17036045 S.H.Yang, A.Galanis, J.Witty, and A.D.Sharrocks (2006).
An extended consensus motif enhances the specificity of substrate modification by SUMO.
  EMBO J, 25, 5083-5093.  
16462746 S.Lee, Y.C.Tsai, R.Mattera, W.J.Smith, M.S.Kostelansky, A.M.Weissman, J.S.Bonifacino, and J.H.Hurley (2006).
Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5.
  Nat Struct Mol Biol, 13, 264-271.
PDB codes: 2fid 2fif
17081985 T.H.Shen, H.K.Lin, P.P.Scaglioni, T.M.Yung, and P.P.Pandolfi (2006).
The mechanisms of PML-nuclear body formation.
  Mol Cell, 24, 331-339.  
16757475 Y.Uchimura, T.Ichimura, J.Uwada, T.Tachibana, S.Sugahara, M.Nakao, and H.Saitoh (2006).
Involvement of SUMO modification in MBD1- and MCAF1-mediated heterochromatin formation.
  J Biol Chem, 281, 23180-23190.  
16714294 Z.Li, R.Cao, M.Wang, M.P.Myers, Y.Zhang, and R.M.Xu (2006).
Structure of a Bmi-1-Ring1B polycomb group ubiquitin ligase complex.
  J Biol Chem, 281, 20643-20649.
PDB code: 2h0d
15949435 D.M.Duda, and B.A.Schulman (2005).
Tag-team SUMO wrestling.
  Mol Cell, 18, 612-614.  
16365295 E.Ozkan, H.Yu, and J.Deisenhofer (2005).
Mechanistic insight into the allosteric activation of a ubiquitin-conjugating enzyme by RING-type ubiquitin ligases.
  Proc Natl Acad Sci U S A, 102, 18890-18895.
PDB codes: 2esk 2eso 2esp 2esq
16120648 J.M.Desterro, L.P.Keegan, E.Jaffray, R.T.Hay, M.A.O'Connell, and M.Carmo-Fonseca (2005).
SUMO-1 modification alters ADAR1 editing activity.
  Mol Biol Cell, 16, 5115-5126.  
16204249 J.Song, Z.Zhang, W.Hu, and Y.Chen (2005).
Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif: a reversal of the bound orientation.
  J Biol Chem, 280, 40122-40129.
PDB code: 2asq
15999109 M.J.Matunis, and C.M.Pickart (2005).
Beginning at the end with SUMO.
  Nat Struct Mol Biol, 12, 565-566.  
16109721 Y.Takahashi, and Y.Kikuchi (2005).
Yeast PIAS-type Ull1/Siz1 is composed of SUMO ligase and regulatory domains.
  J Biol Chem, 280, 35822-35828.  
16300471 Y.Y.Mo, and S.J.Moschos (2005).
Targeting Ubc9 for cancer therapy.
  Expert Opin Ther Targets, 9, 1203-1216.  
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 codes are shown on the right.