PDBsum entry 2grn

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protein Protein-protein interface(s) links
Ligase PDB id
Protein chains
157 a.a. *
157 a.a. *
Waters ×325
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Crystal structure of human rangap1-ubc9
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. Ran gtpase-activating protein 1. Chain: b. Fragment: c-terminal domain (residues 419-587).
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ube2i, ubc9, ubce9. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rangap1.
Biol. unit: Dimer (from PQS)
1.80Å     R-factor:   0.188     R-free:   0.218
Authors: A.A.Yunus,C.D.Lima
Key ref:
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. PubMed id: 16732283 DOI: 10.1038/nsmb1104
24-Apr-06     Release date:   30-May-06    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P63279  (UBC9_HUMAN) -  SUMO-conjugating enzyme UBC9
158 a.a.
157 a.a.
Protein chain
Pfam   ArchSchema ?
P46060  (RAGP1_HUMAN) -  Ran GTPase-activating protein 1
587 a.a.
157 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     synapse   10 terms 
  Biological process     viral reproduction   18 terms 
  Biochemical function     nucleotide binding     17 terms  


DOI no: 10.1038/nsmb1104 Nat Struct Mol Biol 13:491-499 (2006)
PubMed id: 16732283  
Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway.
A.A.Yunus, C.D.Lima.
E2 conjugating proteins that transfer ubiquitin and ubiquitin-like modifiers to substrate lysine residues must first activate the lysine nucleophile for conjugation. Genetic complementation revealed three side chains of the E2 Ubc9 that were crucial for normal growth. Kinetic analysis revealed modest binding defects but substantially lowered catalytic rates for these mutant alleles with respect to wild-type Ubc9. X-ray structures for wild-type and mutant human Ubc9-RanGAP1 complexes showed partial loss of contacts to the substrate lysine in mutant complexes. Computational analysis predicted pK perturbations for the substrate lysine, and Ubc9 mutations weakened pK suppression through improper side chain coordination. Biochemical studies with p53, RanGAP1 and the Nup358/RanBP2 E3 were used to determine rate constants and pK values, confirming both structural and computational predictions. It seems that Ubc9 uses an indirect mechanism to activate lysine for conjugation that may be conserved among E2 family members.
  Selected figure(s)  
Figure 1.
Figure 1. Genetic analysis of the interface between Ubc9 and RanGAP1. (a) Stereo view of the Ubc9 active site in complex with RanGAP1–SUMO^14 (PDB entry 1Z5S) in ribbon and solid-bond representation, depicting Ubc9 residues selected for genetic analysis. Residues are labeled and hydrogen-bonding interactions indicated by dashed lines. Yellow, SUMO-1; pink, RanGAP1; blue, Ubc9. Images generated with PyMOL^44. (b) Serial dilutions of S. cerevisiae ubc9 cultures bearing wild-type (WT) UBC9 or indicated ubc9 alleles containing single or double point mutations were spotted on YPAD agar and tested for growth at 23 °C (top), 30 °C (middle) and 37 °C (bottom) (Note: D127S allele was expressed under yeast endogenous promoter; see text). (c) Western blotting analysis for Smt3 conjugates (top) or Ubc9 (bottom) in strains containing indicated ubc9 alleles.
Figure 2.
Figure 2. Biochemical characterization of wild-type (WT) Ubc9 and mutants. (a) Initial rates of reaction versus p53 substrate concentration, fit to rectangular hyperbolas (Methods), are shown for wild-type Ubc9, Ubc9-N85Q, Ubc9-Y87A and Ubc9-D127A. Left and right y-axes indicate rates for wild-type and mutant enzymes, respectively. (b) Bar charts depicting the kinetic constants apparent K[d] and k[2] for wild-type and mutant Ubc9, plotted on a log scale (see Supplementary Table 1). Error bars in a and b are s.d.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2006, 13, 491-499) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
21474069 A.Saha, S.Lewis, G.Kleiger, B.Kuhlman, and R.J.Deshaies (2011).
Essential role for ubiquitin-ubiquitin-conjugating enzyme interaction in ubiquitin discharge from Cdc34 to substrate.
  Mol Cell, 42, 75-83.  
21092369 D.Barford (2011).
Structure, function and mechanism of the anaphase promoting complex (APC/C).
  Q Rev Biophys, 44, 153-190.  
21532592 D.M.Wenzel, A.Lissounov, P.S.Brzovic, and R.E.Klevit (2011).
UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids.
  Nature, 474, 105-108.  
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
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
20805487 F.Pelisch, J.Gerez, J.Druker, I.E.Schor, M.J.Muñoz, G.Risso, E.Petrillo, B.J.Westman, A.I.Lamond, E.Arzt, and A.Srebrow (2010).
The serine/arginine-rich protein SF2/ASF regulates protein sumoylation.
  Proc Natl Acad Sci U S A, 107, 16119-16124.  
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
20797627 M.C.Rodrigo-Brenni, S.A.Foster, and D.O.Morgan (2010).
Catalysis of lysine 48-specific ubiquitin chain assembly by residues in E2 and ubiquitin.
  Mol Cell, 39, 548-559.  
20704751 M.Sadowski, and B.Sarcevic (2010).
Mechanisms of mono- and poly-ubiquitination: Ubiquitination specificity depends on compatibility between the E2 catalytic core and amino acid residues proximal to the lysine.
  Cell Div, 5, 19.  
20194622 M.Sadowski, R.Suryadinata, X.Lai, J.Heierhorst, and B.Sarcevic (2010).
Molecular basis for lysine specificity in the yeast ubiquitin-conjugating enzyme Cdc34.
  Mol Cell Biol, 30, 2316-2329.  
  20865051 M.Tozluoğlu, E.Karaca, R.Nussinov, and T.Haliloğlu (2010).
A mechanistic view of the role of E3 in sumoylation.
  PLoS Comput Biol, 6, 0.  
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
20014027 T.Ju, W.Bocik, A.Majumdar, and J.R.Tolman (2010).
Solution structure and dynamics of human ubiquitin conjugating enzyme Ube2g2.
  Proteins, 78, 1291-1301.
PDB code: 2kly
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
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.  
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
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.  
19923268 Y.Wang, and M.Dasso (2009).
SUMOylation and deSUMOylation at a glance.
  J Cell Sci, 122, 4249-4252.  
18485863 A.L.Haas, and K.D.Wilkinson (2008).
DeTEKting ubiquitination of APC/C substrates.
  Cell, 133, 570-572.  
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.  
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.  
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.  
18722180 M.K.Summers, B.Pan, K.Mukhyala, and P.K.Jackson (2008).
The unique N terminus of the UbcH10 E2 enzyme controls the threshold for APC activation and enhances checkpoint regulation of the APC.
  Mol Cell, 31, 544-556.  
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.  
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
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.  
17933515 P.Knipscheer, and T.K.Sixma (2007).
Protein-protein interactions regulate Ubl conjugation.
  Curr Opin Struct Biol, 17, 665-673.  
17698585 S.Gazdoiu, K.Yamoah, K.Wu, and Z.Q.Pan (2007).
Human Cdc34 employs distinct sites to coordinate attachment of ubiquitin to a substrate and assembly of polyubiquitin chains.
  Mol Cell Biol, 27, 7041-7052.  
17803232 S.Qin, and H.X.Zhou (2007).
A holistic approach to protein docking.
  Proteins, 69, 743-749.  
17803223 X.Q.Gong, S.Chang, Q.H.Zhang, C.H.Li, L.Z.Shen, X.H.Ma, M.H.Wang, B.Liu, H.Q.He, W.Z.Chen, and C.X.Wang (2007).
A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI.
  Proteins, 69, 859-865.  
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
16757944 P.Knipscheer, and T.K.Sixma (2006).
Divide and conquer: the E2 active site.
  Nat Struct Mol Biol, 13, 474-476.  
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.