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PDBsum entry 2jqz

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protein links
Ligase PDB id
2jqz
Jmol
Contents
Protein chain
131 a.a. *
* Residue conservation analysis
PDB id:
2jqz
Name: Ligase
Title: Solution structure of the c2 domain of human smurf2
Structure: E3 ubiquitin-protein ligase smurf2. Chain: a. Synonym: smad ubiquitination regulatory factor 2, smad- specific e3 ubiquitin ligase 2, hsmurf2. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: smurf2. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_variant: codonplus.
NMR struc: 20 models
Authors: S.Wiesner,A.A.Ogunjimi,H.Wang,D.Rotin,F.Sicheri,J.L.Wrana, J.D.Forman-Kay
Key ref:
S.Wiesner et al. (2007). Autoinhibition of the HECT-type ubiquitin ligase Smurf2 through its C2 domain. Cell, 130, 651-662. PubMed id: 17719543 DOI: 10.1016/j.cell.2007.06.050
Date:
15-Jun-07     Release date:   11-Sep-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9HAU4  (SMUF2_HUMAN) -  E3 ubiquitin-protein ligase SMURF2
Seq:
Struc:
 
Seq:
Struc:
748 a.a.
131 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/j.cell.2007.06.050 Cell 130:651-662 (2007)
PubMed id: 17719543  
 
 
Autoinhibition of the HECT-type ubiquitin ligase Smurf2 through its C2 domain.
S.Wiesner, A.A.Ogunjimi, H.R.Wang, D.Rotin, F.Sicheri, J.L.Wrana, J.D.Forman-Kay.
 
  ABSTRACT  
 
Ubiquitination of proteins is an abundant modification that controls numerous cellular processes. Many Ubiquitin (Ub) protein ligases (E3s) target both their substrates and themselves for degradation. However, the mechanisms regulating their catalytic activity are largely unknown. The C2-WW-HECT-domain E3 Smurf2 downregulates transforming growth factor-beta (TGF-beta) signaling by targeting itself, the adaptor protein Smad7, and TGF-beta receptor kinases for degradation. Here, we demonstrate that an intramolecular interaction between the C2 and HECT domains inhibits Smurf2 activity, stabilizes Smurf2 levels in cells, and similarly inhibits certain other C2-WW-HECT-domain E3s. Using NMR analysis the C2 domain was shown to bind in the vicinity of the catalytic cysteine, where it interferes with Ub thioester formation. The HECT-binding domain of Smad7, which activates Smurf2, antagonizes this inhibitory interaction. Thus, interactions between C2 and HECT domains autoinhibit a subset of HECT-type E3s to protect them and their substrates from futile degradation in cells.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Solution Structure of the Smurf2 C2 Domain
(A) Stereoview of the ensemble of 20 lowest-energy NMR structures out of 100 structures calculated. The backbone trace is shown in gray, while α helices and β strands are highlighted in yellow and blue, respectively.
(B) Ribbon representation of the lowest-energy structure color-coded as in (A). The secondary structure topology of the Smurf2 C2 domain is indicated on the bottom.
(C) Structural superposition of the class II Smurf2 C2 domain (gray) and the class I PKCα C2 domain in complex with Ca^2+-ions and phosphatidyl serine (PDB ID: 1DSY; shown in green). The class I secondary structure topology of the PKCα C2 domain is indicated in green on the bottom.
Figure 3.
Figure 3. Chemical Shift Mapping of the Smurf2 C2 and HECT Domain Interaction Surfaces
(A) Chemical shift mapping of the Smurf2 HECT domain binding site on the C2 domain structure. Residues experiencing significant chemical shift changes (Δδ[Av] ≥ 0.02 ppm) are colored with a linear gradient from white (Δδ[Av] ≤ 0.02 ppm) to red (Δδ[Av] = 0.22 ppm). Spheres represent the nitrogen atoms of affected residues. Average chemical shift changes in proton and nitrogen were calculated as follows: Δδ[Av] = ([Δδ[1H]]^2 + [Δδ[15N]]^2/5)^1/2. Arrows highlight C2 domain residues most affected by ligand binding.
(B) As in (A), but for Ins(1,3,5)P[3] binding and using a linear gradient from white (Δδ[Av] ≤ 0.02 ppm) to blue (Δδ[Av] = 0.22 ppm).
(C) Overlay of representative regions of the ^1H,^13C-HMQC spectra of U-Ile δ1-[1H,^13C]-labeled Smurf2 HECT domain in the absence (black; reference spectrum) and presence of increasing concentrations of unlabeled Smurf2 C2 domain (molar HECT:C2 domain ratios: 1:1 [red]; 1:4 [green]).
(D) Chemical shift mapping of the Smurf2 C2 domain binding site on the HECT domain structure (PDB ID: 1ZVD). Ile residues experiencing significant chemical shift changes are shown in green as sticks, while spheres represent their δ1 methyl carbon atoms. The active site cysteine (C716) located in proximity to the C2 domain binding site (circled) is highlighted in orange.
(E) Deletion of the Smurf2 C2 domain enables Smurf2 Ub thioester formation. Wild-type, catalytically inactive (CA), and ΔC2 Smurf2 truncated by four residues from the C terminus (−4aa) were expressed in bacteria and purified for Ub thioester assays. After an incubation time of 10 min, the reactions were divided in two and stopped with SDS-PAGE loading buffer without (top panel) or with DTT (bottom panel). Smurf2 protein was detected by immunoblotting with α-Smurf2 antibody.
 
  The above figures are reprinted by permission from Cell Press: Cell (2007, 130, 651-662) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22266821 H.Dou, L.Buetow, A.Hock, G.J.Sibbet, K.H.Vousden, and D.T.Huang (2012).
Structural basis for autoinhibition and phosphorylation-dependent activation of c-Cbl.
  Nat Struct Mol Biol, 19, 184-192.
PDB codes: 2y1m 2y1n 4a49 4a4b 4a4c
22301873 S.C.Kales, P.E.Ryan, and S.Lipkowitz (2012).
Cbl exposes its RING finger.
  Nat Struct Mol Biol, 19, 131-133.  
20972579 D.Rotin, and O.Staub (2011).
Role of the ubiquitin system in regulating ion transport.
  Pflugers Arch, 461, 1.  
21245847 E.Argenzio, T.Bange, B.Oldrini, F.Bianchi, R.Peesari, S.Mari, P.P.Di Fiore, M.Mann, and S.Polo (2011).
Proteomic snapshot of the EGF-induced ubiquitin network.
  Mol Syst Biol, 7, 462.  
21294713 G.Ankem, S.Mitra, F.Sun, A.C.Moreno, B.Chutvirasakul, H.F.Azurmendi, L.Li, and D.G.Capelluto (2011).
The C2 domain of Tollip, a Toll-like receptor signalling regulator, exhibits broad preference for phosphoinositides.
  Biochem J, 435, 597-608.  
21505515 H.Kawabe, and N.Brose (2011).
The role of ubiquitylation in nerve cell development.
  Nat Rev Neurosci, 12, 251-268.  
21262463 P.L.Cheng, H.Lu, M.Shelly, H.Gao, and M.M.Poo (2011).
Phosphorylation of E3 ligase Smurf1 switches its substrate preference in support of axon development.
  Neuron, 69, 231-243.  
20026602 A.A.Ogunjimi, S.Wiesner, D.J.Briant, X.Varelas, F.Sicheri, J.Forman-Kay, and J.L.Wrana (2010).
The ubiquitin binding region of the Smurf HECT domain facilitates polyubiquitylation and binding of ubiquitylated substrates.
  J Biol Chem, 285, 6308-6315.  
19997087 B.Liao, and Y.Jin (2010).
Wwp2 mediates Oct4 ubiquitination and its own auto-ubiquitination in a dosage-dependent manner.
  Cell Res, 20, 332-344.  
20862313 E.R.Weiss, E.Popova, H.Yamanaka, H.C.Kim, J.M.Huibregtse, and H.Göttlinger (2010).
Rescue of HIV-1 release by targeting widely divergent NEDD4-type ubiquitin ligases and isolated catalytic HECT domains to Gag.
  PLoS Pathog, 6, 0.  
20479122 M.Krampert, S.R.Chirasani, F.P.Wachs, R.Aigner, U.Bogdahn, J.M.Yingling, C.H.Heldin, L.Aigner, and R.Heuchel (2010).
Smad7 regulates the adult neural stem/progenitor cell pool in a transforming growth factor beta- and bone morphogenetic protein-independent manner.
  Mol Cell Biol, 30, 3685-3694.  
20937913 P.A.Chong, H.Lin, J.L.Wrana, and J.D.Forman-Kay (2010).
Coupling of tandem Smad ubiquitination regulatory factor (Smurf) WW domains modulates target specificity.
  Proc Natl Acad Sci U S A, 107, 18404-18409.
PDB code: 2kxq
20646264 P.Alberts, and D.Rotin (2010).
Regulation of lipid droplet turnover by ubiquitin ligases.
  BMC Biol, 8, 94.  
19373243 P.D.Mace, S.Shirley, and C.L.Day (2010).
Assembling the building blocks: structure and function of inhibitor of apoptosis proteins.
  Cell Death Differ, 17, 46-53.  
20007713 R.K.Pandya, J.R.Partridge, K.R.Love, T.U.Schwartz, and H.L.Ploegh (2010).
A structural element within the HUWE1 HECT domain modulates self-ubiquitination and substrate ubiquitination activities.
  J Biol Chem, 285, 5664-5673.
PDB code: 3h1d
21167755 Y.Yu, and G.S.Hayward (2010).
The ubiquitin E3 ligase RAUL negatively regulates type i interferon through ubiquitination of the transcription factors IRF7 and IRF3.
  Immunity, 33, 863-877.  
19273841 C.M.Quezada, S.W.Hicks, J.E.Galán, and C.E.Stebbins (2009).
A family of Salmonella virulence factors functions as a distinct class of autoregulated E3 ubiquitin ligases.
  Proc Natl Acad Sci U S A, 106, 4864-4869.
PDB code: 3g06
19436320 D.Rotin, and S.Kumar (2009).
Physiological functions of the HECT family of ubiquitin ligases.
  Nat Rev Mol Cell Biol, 10, 398-409.  
19030025 P.Lönn, A.Morén, E.Raja, M.Dahl, and A.Moustakas (2009).
Regulating the stability of TGFbeta receptors and Smads.
  Cell Res, 19, 21-35.  
19255252 Q.Yang, S.P.Chen, X.P.Zhang, H.Wang, C.Zhu, and H.Y.Lin (2009).
Smurf2 participates in human trophoblast cell invasion by inhibiting TGF-beta type I receptor.
  J Histochem Cytochem, 57, 605-612.  
19343052 T.Mund, and H.R.Pelham (2009).
Control of the activity of WW-HECT domain E3 ubiquitin ligases by NDFIP proteins.
  EMBO Rep, 10, 501-507.  
18832381 D.A.Dehring, A.S.Adler, A.Hosseini, and L.Hicke (2008).
A C-terminal Sequence in the Guanine Nucleotide Exchange Factor Sec7 Mediates Golgi Association and Interaction with the Rsp5 Ubiquitin Ligase.
  J Biol Chem, 283, 34188-34196.  
18827983 D.L.Gay, H.Ramón, and P.M.Oliver (2008).
Cbl- and Nedd4-family ubiquitin ligases: balancing tolerance and immunity.
  Immunol Res, 42, 51-64.  
18805092 D.M.Duda, L.A.Borg, D.C.Scott, H.W.Hunt, M.Hammel, and B.A.Schulman (2008).
Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation.
  Cell, 134, 995.
PDB codes: 3dpl 3dqv
18927080 E.Fukunaga, Y.Inoue, S.Komiya, K.Horiguchi, K.Goto, M.Saitoh, K.Miyazawa, D.Koinuma, A.Hanyu, and T.Imamura (2008).
Smurf2 Induces Ubiquitin-dependent Degradation of Smurf1 to Prevent Migration of Breast Cancer Cells.
  J Biol Chem, 283, 35660-35667.  
18321968 H.Y.Chung, E.Morita, U.von Schwedler, B.Müller, H.G.Kräusslich, and W.I.Sundquist (2008).
NEDD4L overexpression rescues the release and infectivity of human immunodeficiency virus type 1 constructs lacking PTAP and YPXL late domains.
  J Virol, 82, 4884-4897.  
18387785 K.H.Wrighton, and X.H.Feng (2008).
To (TGF)beta or not to (TGF)beta: fine-tuning of Smad signaling via post-translational modifications.
  Cell Signal, 20, 1579-1591.  
18641638 K.Lu, X.Yin, T.Weng, S.Xi, L.Li, G.Xing, X.Cheng, X.Yang, L.Zhang, and F.He (2008).
Targeting WW domains linker of HECT-type ubiquitin ligase Smurf1 for activation by CKIP-1.
  Nat Cell Biol, 10, 994.  
18723677 K.Yamoah, T.Oashi, A.Sarikas, S.Gazdoiu, R.Osman, and Z.Q.Pan (2008).
Autoinhibitory regulation of SCF-mediated ubiquitination by human cullin 1's C-terminal tail.
  Proc Natl Acad Sci U S A, 105, 12230-12235.  
18772139 M.Rost, T.Döring, and R.Prange (2008).
{gamma}2-Adaptin, a Ubiquitin-interacting Adaptor, Is a Substrate to Coupled Ubiquitination by the Ubiquitin Ligase Nedd4 and Functions in the Endosomal Pathway.
  J Biol Chem, 283, 32119-32130.  
18784070 P.D.Mace, K.Linke, R.Feltham, F.R.Schumacher, C.A.Smith, D.L.Vaux, J.Silke, and C.L.Day (2008).
Structures of the cIAP2 RING Domain Reveal Conformational Changes Associated with Ubiquitin-conjugating Enzyme (E2) Recruitment.
  J Biol Chem, 283, 31633-31640.
PDB codes: 3eb5 3eb6
18567580 R.Guo, M.Yamashita, Q.Zhang, Q.Zhou, D.Chen, D.G.Reynolds, H.A.Awad, L.Yanoso, L.Zhao, E.M.Schwarz, Y.E.Zhang, B.F.Boyce, and L.Xing (2008).
Ubiquitin Ligase Smurf1 Mediates Tumor Necrosis Factor-induced Systemic Bone Loss by Promoting Proteasomal Degradation of Bone Morphogenetic Signaling Proteins.
  J Biol Chem, 283, 23084-23092.  
19013267 S.Polo, and P.P.Di Fiore (2008).
Finding the right partner: science or ART?
  Cell, 135, 590-592.  
18808420 Y.Inoue, and T.Imamura (2008).
Regulation of TGF-beta family signaling by E3 ubiquitin ligases.
  Cancer Sci, 99, 2107-2112.  
18321969 Y.Usami, S.Popov, E.Popova, and H.G.Göttlinger (2008).
Efficient and specific rescue of human immunodeficiency virus type 1 budding defects by a Nedd4-like ubiquitin ligase.
  J Virol, 82, 4898-4907.  
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.