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PDBsum entry 1th0
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protein Protein-protein interface(s) links
Cell cycle, hydrolase PDB id
1th0

 

 

 

 

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Contents
Protein chain
226 a.a. *
Waters ×209
* Residue conservation analysis
PDB id:
1th0
Name: Cell cycle, hydrolase
Title: Structure of human senp2
Structure: Sentrin-specific protease 2. Chain: a, b. Fragment: catalytic domain. Synonym: sentrin/sumo-specific protease senp2. Smt3-specific isopeptidase 2. Smt3ip2. Axam2. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: senp2, kiaa1331. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.20Å     R-factor:   0.210     R-free:   0.247
Authors: D.Reverter,C.D.Lima
Key ref:
D.Reverter and C.D.Lima (2004). A basis for SUMO protease specificity provided by analysis of human Senp2 and a Senp2-SUMO complex. Structure, 12, 1519-1531. PubMed id: 15296745 DOI: 10.1016/j.str.2004.05.023
Date:
31-May-04     Release date:   14-Sep-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9HC62  (SENP2_HUMAN) -  Sentrin-specific protease 2 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		589 a.a.
226 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.22.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/j.str.2004.05.023 Structure 12:1519-1531 (2004)
PubMed id: 15296745  
 
 
A basis for SUMO protease specificity provided by analysis of human Senp2 and a Senp2-SUMO complex.
D.Reverter, C.D.Lima.
 
  ABSTRACT  
 
Modification of cellular proteins by the ubiquitin-like protein SUMO is essential for nuclear metabolism and cell cycle progression in yeast. X-ray structures of the human Senp2 catalytic protease domain and of a covalent thiohemiacetal transition-state complex obtained between the Senp2 catalytic domain and SUMO-1 revealed details of the respective protease and substrate surfaces utilized in interactions between these two proteins. Comparative biochemical and structural analysis between Senp2 and the yeast SUMO protease Ulp1 revealed differential abilities to process SUMO-1, SUMO-2, and SUMO-3 in maturation and deconjugation reactions. Further biochemical characterization of the three SUMO isoforms into which an additional Gly-Gly di-peptide was inserted, or whereby the respective SUMO tails from the three isoforms were swapped, suggests a strict dependence for SUMO isopeptidase activity on residues C-terminal to the conserved Gly-Gly motif and preferred cleavage site for SUMO proteases.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Structural Superposition of Senp2 and the Senp2-SUMO-1 ComplexStereo representation of Senp2 alone (light blue) and Senp2 (dark blue) in complex with SUMO-1 made by superimposing the respective N-terminal Senp2 subdomains (see text for amino acid numbers). SUMO-1 is represented by a thin gray line. The Senp2 residues involved in interactions with SUMO-1 are labeled and shown in bond representation.
 
  The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 1519-1531) copyright 2004.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23175280 C.M.Hickey, N.R.Wilson, and M.Hochstrasser (2012).
Function and regulation of SUMO proteases.
  Nat Rev Mol Cell Biol, 13, 755-766.  
20547879 D.D.Raymond, M.E.Piper, S.R.Gerrard, and J.L.Smith (2010).
Structure of the Rift Valley fever virus nucleocapsid protein reveals another architecture for RNA encapsidation.
  Proc Natl Acad Sci U S A, 107, 11769-11774.
PDB code: 3lyf
  20087442 E.Van Damme, K.Laukens, T.H.Dang, and X.Van Ostade (2010).
A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamics.
  Int J Biol Sci, 6, 51-67.  
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.  
20811381 M.Drag, and G.S.Salvesen (2010).
Emerging principles in protease-based drug discovery.
  Nat Rev Drug Discov, 9, 690-701.  
20506313 R.Senturia, M.Faller, S.Yin, J.A.Loo, D.Cascio, M.R.Sawaya, D.Hwang, R.T.Clubb, and F.Guo (2010).
Structure of the dimerization domain of DiGeorge critical region 8.
  Protein Sci, 19, 1354-1365.
PDB code: 3le4
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
20544217 Y.C.Shin, B.Y.Liu, J.Y.Tsai, J.T.Wu, L.K.Chang, and S.C.Chang (2010).
Biochemical characterization of the small ubiquitin-like modifiers of Chlamydomonas reinhardtii.
  Planta, 232, 649-662.  
19656081 C.B.Carlson, R.A.Horton, and K.W.Vogel (2009).
A toolbox approach to high-throughput TR-FRET-based SUMOylation and DeSUMOylation assays.
  Assay Drug Dev Technol, 7, 348-355.  
19107421 D.Reverter, and C.D.Lima (2009).
Preparation of SUMO proteases and kinetic analysis using endogenous substrates.
  Methods Mol Biol, 497, 225-239.  
19008217 E.T.Yeh (2009).
SUMOylation and De-SUMOylation: Wrestling with Life's Processes.
  J Biol Chem, 284, 8223-8227.  
19434753 J.Pei, and N.V.Grishin (2009).
The Rho GTPase inactivation domain in Vibrio cholerae MARTX toxin has a circularly permuted papain-like thiol protease fold.
  Proteins, 77, 413-419.  
20041154 Y.Wang, D.Mukhopadhyay, S.Mathew, T.Hasebe, R.A.Heimeier, Y.Azuma, N.Kolli, Y.B.Shi, K.D.Wilkinson, and M.Dasso (2009).
Identification and developmental expression of Xenopus laevis SUMO proteases.
  PLoS One, 4, e8462.  
19923268 Y.Wang, and M.Dasso (2009).
SUMOylation and deSUMOylation at a glance.
  J Cell Sci, 122, 4249-4252.  
19186998 Z.Xu, H.Y.Chan, W.L.Lam, K.H.Lam, L.S.Lam, T.B.Ng, and S.W.Au (2009).
SUMO proteases: redox regulation and biological consequences.
  Antioxid Redox Signal, 11, 1453-1484.  
18799455 C.D.Lima, and D.Reverter (2008).
Structure of the Human SENP7 Catalytic Domain and Poly-SUMO Deconjugation Activities for SENP6 and SENP7.
  J Biol Chem, 283, 32045-32055.
PDB code: 3eay
18538659 E.Meulmeester, M.Kunze, H.H.Hsiao, H.Urlaub, and F.Melchior (2008).
Mechanism and consequences for paralog-specific sumoylation of ubiquitin-specific protease 25.
  Mol Cell, 30, 610-619.  
18666185 M.Drag, and G.S.Salvesen (2008).
DeSUMOylating enzymes--SENPs.
  IUBMB Life, 60, 734-742.  
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.  
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.  
17499995 D.Mukhopadhyay, and M.Dasso (2007).
Modification in reverse: the SUMO proteases.
  Trends Biochem Sci, 32, 286-295.  
17591783 J.Mikolajczyk, M.Drag, M.Békés, J.T.Cao, Z.Ronai, and G.S.Salvesen (2007).
Small ubiquitin-related modifier (SUMO)-specific proteases: profiling the specificities and activities of human SENPs.
  J Biol Chem, 282, 26217-26224.  
17428805 M.Ihara, H.Koyama, Y.Uchimura, H.Saitoh, and A.Kikuchi (2007).
Noncovalent binding of small ubiquitin-related modifier (SUMO) protease to SUMO is necessary for enzymatic activities and cell growth.
  J Biol Chem, 282, 16465-16475.  
17204475 R.Chosed, D.R.Tomchick, C.A.Brautigam, S.Mukherjee, V.S.Negi, M.Machius, and K.Orth (2007).
Structural analysis of Xanthomonas XopD provides insights into substrate specificity of ubiquitin-like protein proteases.
  J Biol Chem, 282, 6773-6782.
PDB codes: 2oiv 2oix
17932034 T.Bawa-Khalfe, J.Cheng, Z.Wang, and E.T.Yeh (2007).
Induction of the SUMO-specific protease 1 transcription by the androgen receptor in prostate cancer cells.
  J Biol Chem, 282, 37341-37349.  
17960327 V.Katritch, C.M.Byrd, V.Tseitin, D.Dai, E.Raush, M.Totrov, R.Abagyan, R.Jordan, and D.E.Hruby (2007).
Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches.
  J Comput Aided Mol Des, 21, 549-558.  
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
17146457 D.T.Huang, and B.A.Schulman (2006).
Breaking up with a kinky SUMO.
  Nat Struct Mol Biol, 13, 1045-1047.  
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.  
16913834 T.Sulea, H.A.Lindner, and R.Ménard (2006).
Structural aspects of recently discovered viral deubiquitinating activities.
  Biol Chem, 387, 853-862.  
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
16183633 K.Sugawara, N.N.Suzuki, Y.Fujioka, N.Mizushima, Y.Ohsumi, and F.Inagaki (2005).
Structural basis for the specificity and catalysis of human Atg4B responsible for mammalian autophagy.
  J Biol Chem, 280, 40058-40065.
PDB code: 2cy7
15660128 L.M.Lois, and C.D.Lima (2005).
Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1.
  EMBO J, 24, 439-451.
PDB codes: 1y8q 1y8r
15775960 L.N.Shen, H.Liu, C.Dong, D.Xirodimas, J.H.Naismith, and R.T.Hay (2005).
Structural basis of NEDD8 ubiquitin discrimination by the deNEDDylating enzyme NEDP1.
  EMBO J, 24, 1341-1351.
PDB codes: 2bkq 2bkr
15870296 S.Chupreta, S.Holmstrom, L.Subramanian, and J.A.Iñiguez-Lluhí (2005).
A small conserved surface in SUMO is the critical structural determinant of its transcriptional inhibitory properties.
  Mol Cell Biol, 25, 4272-4282.  
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.

 

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