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PDBsum entry 1fxt

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protein Protein-protein interface(s) links
Ligase PDB id
1fxt
Jmol
Contents
Protein chains
149 a.a. *
76 a.a. *
* Residue conservation analysis
PDB id:
1fxt
Name: Ligase
Title: Structure of a conjugating enzyme-ubiquitin thiolester complex
Structure: Ubiquitin-conjugating enzyme e2-24 kda. Chain: a. Engineered: yes. Ubiquitin. Chain: b. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606.
NMR struc: 1 models
Authors: K.S.Hamilton,G.S.Shaw,R.S.Williams,J.T.Huzil,S.Mckenna, C.Ptak,M.Glover,M.J.Ellison
Key ref:
K.S.Hamilton et al. (2001). Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail. Structure, 9, 897-904. PubMed id: 11591345 DOI: 10.1016/S0969-2126(01)00657-8
Date:
26-Sep-00     Release date:   10-Oct-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P21734  (UBC1_YEAST) -  Ubiquitin-conjugating enzyme E2 1
Seq:
Struc:
215 a.a.
149 a.a.
Protein chain
Pfam   ArchSchema ?
P0CG48  (UBC_HUMAN) -  Polyubiquitin-C
Seq:
Struc:
 
Seq:
Struc:
685 a.a.
76 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain A: E.C.6.3.2.19  - Ubiquitin--protein ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine
ATP
+ ubiquitin
+ protein lysine
= AMP
+ diphosphate
+ protein N-ubiquityllysine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     acid-amino acid ligase activity     1 term  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(01)00657-8 Structure 9:897-904 (2001)
PubMed id: 11591345  
 
 
Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail.
K.S.Hamilton, M.J.Ellison, K.R.Barber, R.S.Williams, J.T.Huzil, S.McKenna, C.Ptak, M.Glover, G.S.Shaw.
 
  ABSTRACT  
 
BACKGROUND: Ubiquitin-conjugating enzymes (E2s) are central enzymes involved in ubiquitin-mediated protein degradation. During this process, ubiquitin (Ub) and the E2 protein form an unstable E2-Ub thiolester intermediate prior to the transfer of ubiquitin to an E3-ligase protein and the labeling of a substrate for degradation. A series of complex interactions occur among the target substrate, ubiquitin, E2, and E3 in order to efficiently facilitate the transfer of the ubiquitin molecule. However, due to the inherent instability of the E2-Ub thiolester, the structural details of this complex intermediate are not known. RESULTS: A three-dimensional model of the E2-Ub thiolester intermediate has been determined for the catalytic domain of the E2 protein Ubc1 (Ubc1(Delta450)) and ubiquitin from S. cerevisiae. The interface of the E2-Ub intermediate was determined by kinetically monitoring thiolester formation by 1H-(15)N HSQC spectra by using combinations of 15N-labeled and unlabeled Ubc1(Delta450) and Ub proteins. By using the surface interface as a guide and the X-ray structures of Ub and the 1.9 A structure of Ubc1(Delta450) determined here, docking simulations followed by energy minimization were used to produce the first model of a E2-Ub thiolester intermediate. CONCLUSIONS: Complementary surfaces were found on the E2 and Ub proteins whereby the C terminus of Ub wraps around the E2 protein terminating in the thiolester between C88 (Ubc1(Delta450)) and G76 (Ub). The model supports in vivo and in vitro experiments of E2 derivatives carrying surface residue substitutions. Furthermore, the model provides insights into the arrangement of Ub, E2, and E3 within a ternary targeting complex.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Model of the E2-Ub Thiolester IntermediateThe model was determined by Monte Carlo docking as described in Experimental Procedures. The model shows (a) side and (b) end orientation views of helix a2 in the E2 molecule. Residues are indicated on both E2 and Ub to indicate important side chain-side chain interactions that arise at the protein-protein interface, as described in the text. In both figures, the thiol-forming C88 residue in E2 is a shown as a yellow ball-and-stick representation near the (a) center and (b) top of the complex

 
  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 897-904) copyright 2001.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
21453497 A.Lass, R.Cocklin, K.M.Scaglione, M.Skowyra, S.Korolev, M.Goebl, and D.Skowyra (2011).
The loop-less tmCdc34 E2 mutant defective in polyubiquitination in vitro and in vivo supports yeast growth in a manner dependent on Ubp14 and Cka2.
  Cell Div, 6, 7.  
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.  
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.  
20154706 A.R.Cole, L.P.Lewis, and H.Walden (2010).
The structure of the catalytic subunit FANCL of the Fanconi anemia core complex.
  Nat Struct Mol Biol, 17, 294-298.
PDB code: 3k1l
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
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.  
20053359 N.G.Sgourakis, M.M.Patel, A.E.Garcia, G.I.Makhatadze, and S.A.McCallum (2010).
Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain.
  J Mol Biol, 396, 1128-1144.
PDB code: 2kdi
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
19101823 G.Liu, F.Forouhar, A.Eletsky, H.S.Atreya, J.M.Aramini, R.Xiao, Y.J.Huang, M.Abashidze, J.Seetharaman, J.Liu, B.Rost, T.Acton, G.T.Montelione, J.F.Hunt, and T.Szyperski (2009).
NMR and X-RAY structures of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1) reveal structural and functional conservation in the metazoan UFM1-UBA5-UFC1 ubiquination pathway.
  J Struct Funct Genomics, 10, 127-136.
PDB codes: 2k07 3e2g 3evx
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
19602541 Y.Zhou, Z.W.Carpenter, G.Brennan, and J.R.Nambu (2009).
The unique Morgue ubiquitination protein is conserved in a diverse but restricted set of invertebrates.
  Mol Biol Evol, 26, 2245-2259.  
18545708 N.Ponts, J.Yang, D.W.Chung, J.Prudhomme, T.Girke, P.Horrocks, and K.G.Le Roch (2008).
Deciphering the ubiquitin-mediated pathway in apicomplexan parasites: a potential strategy to interfere with parasite virulence.
  PLoS ONE, 3, e2386.  
19055796 P.Slama, I.Filippis, and M.Lappe (2008).
Detection of protein catalytic residues at high precision using local network properties.
  BMC Bioinformatics, 9, 517.  
19007434 S.Beaudenon, and J.M.Huibregtse (2008).
HPV E6, E6AP and cervical cancer.
  BMC Biochem, 9, S4.  
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.  
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
17951259 J.T.Huzil, R.Pannu, C.Ptak, G.Garen, and M.J.Ellison (2007).
Direct catalysis of lysine 48-linked polyubiquitin chains by the ubiquitin-activating enzyme.
  J Biol Chem, 282, 37454-37460.  
17562869 K.M.Scaglione, P.K.Bansal, A.E.Deffenbaugh, A.Kiss, J.M.Moore, S.Korolev, R.Cocklin, M.Goebl, K.Kitagawa, and D.Skowyra (2007).
SCF E3-mediated autoubiquitination negatively regulates activity of Cdc34 E2 but plays a nonessential role in the catalytic cycle in vitro and in vivo.
  Mol Cell Biol, 27, 5860-5870.  
17491593 P.Knipscheer, W.J.van Dijk, J.V.Olsen, M.Mann, and T.K.Sixma (2007).
Noncovalent interaction between Ubc9 and SUMO promotes SUMO chain formation.
  EMBO J, 26, 2797-2807.
PDB code: 2uyz
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.  
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
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
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.  
16543155 P.S.Brzovic, A.Lissounov, D.E.Christensen, D.W.Hoyt, and R.E.Klevit (2006).
A UbcH5/ubiquitin noncovalent complex is required for processive BRCA1-directed ubiquitination.
  Mol Cell, 21, 873-880.
PDB code: 2fuh
16518384 S.L.Alam, and W.I.Sundquist (2006).
Two new structures of Ub-receptor complexes. U2.
  Nat Struct Mol Biol, 13, 186-188.  
15723079 A.Pichler, P.Knipscheer, E.Oberhofer, W.J.van Dijk, R.Körner, J.V.Olsen, S.Jentsch, F.Melchior, and T.K.Sixma (2005).
SUMO modification of the ubiquitin-conjugating enzyme E2-25K.
  Nat Struct Mol Biol, 12, 264-269.
PDB codes: 2bep 2bf8
15772086 C.Tsui, A.Raguraj, and C.M.Pickart (2005).
Ubiquitin binding site of the ubiquitin E2 variant (UEV) protein Mms2 is required for DNA damage tolerance in the yeast RAD6 pathway.
  J Biol Chem, 280, 19829-19835.  
15931224 D.Reverter, and C.D.Lima (2005).
Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex.
  Nature, 435, 687-692.
PDB code: 1z5s
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
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
15722448 F.Massi, M.J.Grey, and A.G.Palmer (2005).
Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1rho relaxation experiments.
  Protein Sci, 14, 735-742.  
16064137 L.Hicke, H.L.Schubert, and C.P.Hill (2005).
Ubiquitin-binding domains.
  Nat Rev Mol Cell Biol, 6, 610-621.  
15749714 L.Pastushok, T.F.Moraes, M.J.Ellison, and W.Xiao (2005).
A single Mms2 "key" residue insertion into a Ubc13 pocket determines the interface specificity of a human Lys63 ubiquitin conjugation complex.
  J Biol Chem, 280, 17891-17900.  
16014632 N.Merkley, K.R.Barber, and G.S.Shaw (2005).
Ubiquitin manipulation by an E2 conjugating enzyme using a novel covalent intermediate.
  J Biol Chem, 280, 31732-31738.  
16207353 P.J.Stogios, G.S.Downs, J.J.Jauhal, S.K.Nandra, and G.G.Privé (2005).
Sequence and structural analysis of BTB domain proteins.
  Genome Biol, 6, R82.  
16142244 Z.M.Eletr, D.T.Huang, D.M.Duda, B.A.Schulman, and B.Kuhlman (2005).
E2 conjugating enzymes must disengage from their E1 enzymes before E3-dependent ubiquitin and ubiquitin-like transfer.
  Nat Struct Mol Biol, 12, 933-934.  
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
15361859 D.T.Huang, D.W.Miller, R.Mathew, R.Cassell, J.M.Holton, M.F.Roussel, and B.A.Schulman (2004).
A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8.
  Nat Struct Mol Biol, 11, 927-935.
PDB code: 1tt5
15044434 H.Teo, D.B.Veprintsev, and R.L.Williams (2004).
Structural insights into endosomal sorting complex required for transport (ESCRT-I) recognition of ubiquitinated proteins.
  J Biol Chem, 279, 28689-28696.
PDB code: 1uzx
15377232 J.Smalle, and R.D.Vierstra (2004).
The ubiquitin 26S proteasome proteolytic pathway.
  Annu Rev Plant Biol, 55, 555-590.  
15328341 N.Merkley, and G.S.Shaw (2004).
Solution structure of the flexible class II ubiquitin-conjugating enzyme Ubc1 provides insights for polyubiquitin chain assembly.
  J Biol Chem, 279, 47139-47147.
PDB code: 1tte
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.  
15053872 W.I.Sundquist, H.L.Schubert, B.N.Kelly, G.C.Hill, J.M.Holton, and C.P.Hill (2004).
Ubiquitin recognition by the human TSG101 protein.
  Mol Cell, 13, 783-789.
PDB code: 1s1q
12944097 B.R.Wong, F.Parlati, K.Qu, S.Demo, T.Pray, J.Huang, D.G.Payan, and M.K.Bennett (2003).
Drug discovery in the ubiquitin regulatory pathway.
  Drug Discov Today, 8, 746-754.  
12535537 M.A.Verdecia, C.A.Joazeiro, N.J.Wells, J.L.Ferrer, M.E.Bowman, T.Hunter, and J.P.Noel (2003).
Conformational flexibility underlies ubiquitin ligation mediated by the WWP1 HECT domain E3 ligase.
  Mol Cell, 11, 249-259.
PDB code: 1nd7
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.  
12569095 S.McKenna, T.Moraes, L.Pastushok, C.Ptak, W.Xiao, L.Spyracopoulos, and M.J.Ellison (2003).
An NMR-based model of the ubiquitin-bound human ubiquitin conjugation complex Mms2.Ubc13. The structural basis for lysine 63 chain catalysis.
  J Biol Chem, 278, 13151-13158.  
12553912 S.Orlicky, X.Tang, A.Willems, M.Tyers, and F.Sicheri (2003).
Structural basis for phosphodependent substrate selection and orientation by the SCFCdc4 ubiquitin ligase.
  Cell, 112, 243-256.
PDB code: 1nex
12861024 X.Varelas, C.Ptak, and M.J.Ellison (2003).
Cdc34 self-association is facilitated by ubiquitin thiolester formation and is required for its catalytic activity.
  Mol Cell Biol, 23, 5388-5400.  
12354763 K.P.Bencsath, M.S.Podgorski, V.R.Pagala, C.A.Slaughter, and B.A.Schulman (2002).
Identification of a multifunctional binding site on Ubc9p required for Smt3p conjugation.
  J Biol Chem, 277, 47938-47945.  
11931752 M.Hochstrasser (2002).
New structural clues to substrate specificity in the "ubiquitin system".
  Mol Cell, 9, 453-454.  
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
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.