PDBsum entry 1gt9

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
357 a.a. *
SO4 ×2
_CA ×2
Waters ×566
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: High resolution crystal structure of a thermostable serine-carboxyl type proteinase, kumamolisin (kscp)
Structure: Kumamolysin. Chain: 1, 2. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: bacterium found in hotspring water near volcanoes
Biol. unit: Monomer (from PDB file)
1.38Å     R-factor:   0.194     R-free:   0.208
Authors: M.Comellas-Bigler,P.Fuentes-Prior,K.Maskos,R.Huber,H.Oyama, K.Uchida,B.M.Dunn,K.Oda,W.Bode
Key ref:
M.Comellas-Bigler et al. (2002). The 1.4 a crystal structure of kumamolysin: a thermostable serine-carboxyl-type proteinase. Structure, 10, 865-876. PubMed id: 12057200 DOI: 10.1016/S0969-2126(02)00772-4
14-Jan-02     Release date:   13-Jun-02    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q8RR56  (Q8RR56_9BACI) -  Kumamolisin
552 a.a.
357 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     serine-type endopeptidase activity     1 term  


DOI no: 10.1016/S0969-2126(02)00772-4 Structure 10:865-876 (2002)
PubMed id: 12057200  
The 1.4 a crystal structure of kumamolysin: a thermostable serine-carboxyl-type proteinase.
M.Comellas-Bigler, P.Fuentes-Prior, K.Maskos, R.Huber, H.Oyama, K.Uchida, B.M.Dunn, K.Oda, W.Bode.
Kumamolysin is a thermostable endopeptidase from Bacillus novosp. MN-32, exhibiting maximal proteolytic activity around pH 3. It belongs to the newly identified family of serine-carboxyl proteinases, which also includes CLN2, a human lysosomal homolog recently implicated in a fatal neurodegenerative disease. Kumamolysin and its complexes with two aldehyde inhibitors were crystallized, and their three-dimensional structures were solved and refined with X-ray data to 1.4 A resolution. As its Pseudomonas homolog, kumamolysin exhibits a Ser/Glu/Asp catalytic triad with particularly short interconnecting hydrogen bonds and an oxyanion hole enabling the reactive serine to attack substrate peptide bonds at quite acidic pH. An additional Glu/Trp pair, unique to kumamolysin, might further facilitate proton delocalization during nucleophilic attack, in particular at high temperature.
  Selected figure(s)  
Figure 4.
Figure 4. Electrostatic Surface Representation of KSCPSolid surface representation of the "front" side of KSCP shown in the same orientation as in Figure 1, and of the "back" side, obtained after a rotation of 180 around a vertical axis. The colors indicate the electrostatic surface potential at pH 7 contoured from +20 kT/e (dark blue) to -20 kT/e (dark red). White lines indicate the approximate position of the Ca^2+ binding residues Asp316 and Asp338. The image was generated with GRASP [44].
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 865-876) copyright 2002.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19038966 A.Pal, R.Kraetzner, T.Gruene, M.Grapp, K.Schreiber, M.Grønborg, H.Urlaub, S.Becker, A.R.Asif, J.Gärtner, G.M.Sheldrick, and R.Steinfeld (2009).
Structure of Tripeptidyl-peptidase I Provides Insight into the Molecular Basis of Late Infantile Neuronal Ceroid Lipofuscinosis.
  J Biol Chem, 284, 3976-3984.
PDB code: 3ee6
19038967 J.Guhaniyogi, I.Sohar, K.Das, A.M.Stock, and P.Lobel (2009).
Crystal Structure and Autoactivation Pathway of the Precursor Form of Human Tripeptidyl-peptidase 1, the Enzyme Deficient in Late Infantile Ceroid Lipofuscinosis.
  J Biol Chem, 284, 3985-3997.
PDB code: 3edy
19420694 W.Nishii, K.Kubota, and K.Takahashi (2009).
The P1 and P1' residue specificities of physarolisin I, a serine-carboxyl peptidase from the true slime mold Physarum polycephalum.
  Biosci Biotechnol Biochem, 73, 1168-1171.  
18824507 O.D.Ekici, M.Paetzel, and R.E.Dalbey (2008).
Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration.
  Protein Sci, 17, 2023-2037.  
18083574 M.Koch, S.Camp, T.Collen, D.Avila, J.Salomonsen, H.J.Wallny, A.van Hateren, L.Hunt, J.P.Jacob, F.Johnston, D.A.Marston, I.Shaw, P.R.Dunbar, V.Cerundolo, E.Y.Jones, and J.Kaufman (2007).
Structures of an MHC class I molecule from B21 chickens illustrate promiscuous peptide binding.
  Immunity, 27, 885-899.
PDB codes: 3bev 3bew
17326662 Q.Xu, H.B.Guo, A.Wlodawer, T.Nakayama, and H.Guo (2007).
The QM/MM molecular dynamics and free energy simulations of the acylation reaction catalyzed by the serine-carboxyl peptidase kumamolisin-As.
  Biochemistry, 46, 3784-3792.  
17348030 R.J.Siezen, B.Renckens, and J.Boekhorst (2007).
Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues.
  Proteins, 67, 681-694.  
16704427 A.Okubo, M.Li, M.Ashida, H.Oyama, A.Gustchina, K.Oda, B.M.Dunn, A.Wlodawer, and T.Nakayama (2006).
Processing, catalytic activity and crystal structures of kumamolisin-As with an engineered active site.
  FEBS J, 273, 2563-2576.
PDB codes: 1zvj 1zvk
16669642 Q.Xu, H.Guo, A.Wlodawer, and H.Guo (2006).
The importance of dynamics in substrate-assisted catalysis and specificity.
  J Am Chem Soc, 128, 5994-5995.  
15143070 A.A.Golabek, P.Wujek, M.Walus, S.Bieler, C.Soto, K.E.Wisniewski, and E.Kida (2004).
Maturation of human tripeptidyl-peptidase I in vitro.
  J Biol Chem, 279, 31058-31067.  
15014068 A.Wlodawer, M.Li, A.Gustchina, N.Tsuruoka, M.Ashida, H.Minakata, H.Oyama, K.Oda, T.Nishino, and T.Nakayama (2004).
Crystallographic and biochemical investigations of kumamolisin-As, a serine-carboxyl peptidase with collagenase activity.
  J Biol Chem, 279, 21500-21510.
PDB codes: 1sio 1siu 1sn7
15242582 A.Wlodawer (2004).
How to kill an enzyme (in more ways than one).
  Structure, 12, 1117-1119.  
14702339 P.Wujek, E.Kida, M.Walus, K.E.Wisniewski, and A.A.Golabek (2004).
N-glycosylation is crucial for folding, trafficking, and stability of human tripeptidyl-peptidase I.
  J Biol Chem, 279, 12827-12839.  
14609438 A.Wlodawer, S.R.Durell, M.Li, H.Oyama, K.Oda, and B.M.Dunn (2003).
A model of tripeptidyl-peptidase I (CLN2), a ubiquitous and highly conserved member of the sedolisin family of serine-carboxyl peptidases.
  BMC Struct Biol, 3, 8.
PDB code: 1r60
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.