PDBsum entry 1sio

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protein ligands metals Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
Protein chains
357 a.a. *
SO4 ×3
_CA ×3
Waters ×935
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase inhibitor
Title: Structure of kumamolisin-as complexed with a covalently-boun inhibitor, acipf
Structure: Kumamolisin-as. Chain: a, b, c. Engineered: yes. Ace-ile-pro-phl peptide inhibitor. Chain: d, e, f. Engineered: yes
Source: Alicyclobacillus sendaiensis. Organism_taxid: 192387. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: the peptide was chemically synthesized.
Biol. unit: Dimer (from PQS)
1.80Å     R-factor:   0.173     R-free:   0.243
Authors: M.Li,A.Wlodawer,A.Gustchina,N.Tsuruoka,M.Ashida,H.Minakata,H K.Oda,T.Nishino,T.Nakayama
Key ref:
A.Wlodawer et al. (2004). Crystallographic and biochemical investigations of kumamolisin-As, a serine-carboxyl peptidase with collagenase activity. J Biol Chem, 279, 21500-21510. PubMed id: 15014068 DOI: 10.1074/jbc.M401141200
01-Mar-04     Release date:   30-Mar-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q8GB88  (Q8GB88_9BACL) -  Kumamolisin-As
553 a.a.
357 a.a.
Key:    PfamA 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: 10.1074/jbc.M401141200 J Biol Chem 279:21500-21510 (2004)
PubMed id: 15014068  
Crystallographic and biochemical investigations of kumamolisin-As, a serine-carboxyl peptidase with collagenase activity.
A.Wlodawer, M.Li, A.Gustchina, N.Tsuruoka, M.Ashida, H.Minakata, H.Oyama, K.Oda, T.Nishino, T.Nakayama.
Kumamolisin-As (previously called ScpA) is the first known example of a collagenase from the sedolisin family (MEROPS S53). This enzyme is active at low pH and in elevated temperatures. In this study that used x-ray crystallographic and biochemical methods, we investigated the structural basis of the preference of this enzyme for collagen and the importance of a glutamate residue in the unique catalytic triad (Ser(278)-Glu(78)-Asp(82)) for enzymatic activity. Crystal structures of the uninhibited enzyme and its complex with a covalently bound inhibitor, N-acetyl-isoleucyl-prolyl-phenylalaninal, showed the occurrence of a narrow S2 pocket and a groove that encompasses the active site and is rich in negative charges. Limited endoproteolysis studies of bovine type-I collagen as well as kinetic studies using peptide libraries randomized at P1 and P1', showed very strong preference for arginine at the P1 position, which correlated very well with the presence of a negatively charged residue in the S1 pocket of the enzyme. All of these features, together with those predicted through comparisons with fiddler crab collagenase, a serine peptidase, rationalize the enzyme's preference for collagen. A comparison of the Arrhenius plots of the activities of kumamolisin-As with either collagen or peptides as substrates suggests that collagen should be relaxed before proteolysis can occur. The E78H mutant, in which the catalytic triad was engineered to resemble that of subtilisin, showed only 0.01% activity of the wild-type enzyme, and its structure revealed that Ser(278), His(78), and Asp(82) do not interact with each other; thus, the canonical catalytic triad is disrupted.
  Selected figure(s)  
Figure 5.
FIG. 5. A superposition of the active sites of four proteases. Kumamolisin-As with bound AcIPF is shown in blue; sedolisin and bound tyrostatin are colored red and brown, respectively; subtilisin is shown in lilac, and its inhibitor eglin is shown in violet. Fiddler crab collagenase is colored green, whereas its inhibitor ecotin is orange. The C atoms of kumamolisin-As, sedolisin, and subtilisin were superimposed with the program ALIGN (34). Superposition of kumamolisin-As with fiddler crab collagenase is described under "Results."
Figure 6.
FIG. 6. Superposition of kumamolisin-As and fiddler crab collagenase. The two structures were superimposed as described under "Results." The main chain tracing of kumamolisin-As and fiddler crab collagenase is shown as red and blue ribbons, respectively, and the superimposed side chains of the active sites residues are shown as sticks in corresponding colors. The strands 127-132 in kumamolisin-As and 213-218 in collagenase are emphasized in black (see under "Results"). The inhibitor AcIPF is shown in gold, and a fragment of ecotin is shown in green.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 21500-21510) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
19223444 M.A.Ditzler, J.Sponer, and N.G.Walter (2009).
Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.
  RNA, 15, 560-575.  
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
16952949 Y.Itoi, M.Horinaka, Y.Tsujimoto, H.Matsui, and K.Watanabe (2006).
Characteristic features in the structure and collagen-binding ability of a thermophilic collagenolytic protease from the thermophile Geobacillus collagenovorans MO-1.
  J Bacteriol, 188, 6572-6579.  
17027867 Y.Suzuki, Y.Tsujimoto, H.Matsui, and K.Watanabe (2006).
Decomposition of extremely hard-to-degrade animal proteins by thermophilic bacteria.
  J Biosci Bioeng, 102, 73-81.  
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.