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PDBsum entry 1wsd
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protein ligands metals links
Hydrolase PDB id
1wsd

 

 

 

 

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Contents
Protein chain
269 a.a. *
Ligands
SO4
Metals
_CA
Waters ×124
* Residue conservation analysis
PDB id:
1wsd
Name: Hydrolase
Title: Alkaline m-protease form i crystal structure
Structure: M-protease. Chain: a. Engineered: yes
Source: Bacillus clausii. Organism_taxid: 66692. Strain: ksm-k16. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.50Å     R-factor:   0.172     R-free:   0.193
Authors: T.Shirai,A.Suzuki,T.Yamane,T.Ashida,T.Kobayashi,J.Hitomi,S.Ito
Key ref: T.Shirai et al. (1997). High-resolution crystal structure of M-protease: phylogeny aided analysis of the high-alkaline adaptation mechanism. Protein Eng, 10, 627-634. PubMed id: 9278275
Date:
05-Nov-04     Release date:   16-Nov-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q99405  (PRTM_BACSK) -  M-protease from Shouchella clausii (strain KSM-K16)
Seq:
Struc: 		380 a.a.
269 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Protein Eng 10:627-634 (1997)
PubMed id: 9278275  
 
 
High-resolution crystal structure of M-protease: phylogeny aided analysis of the high-alkaline adaptation mechanism.
T.Shirai, A.Suzuki, T.Yamane, T.Ashida, T.Kobayashi, J.Hitomi, S.Ito.
 
  ABSTRACT  
 
M-protease is a subtilisin-family serine protease produced by an alkaliphilic Bacillus sp. strain. Optimal enzymatic activity of the protein occurs at pH 12.3. The crystal structure of M-protease (space group P2(1)2(1)2(1), a = 62.3, b = 75.5, c = 47.2 A) has been refined to a crystallographic R-factor of 17.2% at 1.5 A resolution. The alkaline adaptation mechanism of the enzyme was analyzed. Molecular phylogeny construction was used to determine the amino acid substitutions that occurred during the high-alkaline adaptation process. This analysis revealed a decrease in the number of negatively charged amino acids (aspartic acid and glutamic acid) and lysine residues and an increase in arginine and neutral hydrophilic amino acids (histidine, asparagine and glutamine) residues during the course of adaptation. These substitutions increased the isoelectric point of M-protease. Some of the acquired arginine residues form hydrogen bonds or ion pairs to combine both N- and C-terminal regions of M-protease. The substituted residues are localized to a hemisphere of the globular protein molecule where positional shifts of peptide segments, relative to those of the less alkaliphilic subtilisin Carlsberg, are observed. The biased distribution and interactions caused by the substituted residues seem to be responsible for stabilization of the conformation in a high-alkaline condition.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20543007 S.J.Wu, J.Luo, K.T.O'Neil, J.Kang, E.R.Lacy, G.Canziani, A.Baker, M.Huang, Q.M.Tang, T.S.Raju, S.A.Jacobs, A.Teplyakov, G.L.Gilliland, and Y.Feng (2010).
Structure-based engineering of a monoclonal antibody for improved solubility.
  Protein Eng Des Sel, 23, 643-651.  
19214652 A.Hayashi, H.Nagafuchi, I.Ito, K.Hirota, M.Yoshida, and S.Ozaki (2009).
Lupus antibodies to the HMGB1 chromosomal protein: epitope mapping and association with disease activity.
  Mod Rheumatol, 19, 283-292.  
19352020 H.Umemoto, Ihsanawati, M.Inami, R.Yatsunami, T.Fukui, T.Kumasaka, N.Tanaka, and S.Nakamura (2009).
Improvement of alkaliphily of Bacillus alkaline xylanase by introducing amino acid substitutions both on catalytic cleft and protein surface.
  Biosci Biotechnol Biochem, 73, 965-967.  
18371216 M.Zhou, J.Boekhorst, C.Francke, and R.J.Siezen (2008).
LocateP: genome-scale subcellular-location predictor for bacterial proteins.
  BMC Bioinformatics, 9, 173.  
17630120 K.Saeki, K.Ozaki, T.Kobayashi, and S.Ito (2007).
Detergent alkaline proteases: enzymatic properties, genes, and crystal structures.
  J Biosci Bioeng, 103, 501-508.  
17154418 T.Shirai, K.Igarashi, T.Ozawa, H.Hagihara, T.Kobayashi, K.Ozaki, and S.Ito (2007).
Ancestral sequence evolutionary trace and crystal structure analyses of alkaline alpha-amylase from Bacillus sp. KSM-1378 to clarify the alkaline adaptation process of proteins.
  Proteins, 66, 600-610.
PDB code: 2die
17429572 Y.Kageyama, Y.Takaki, S.Shimamura, S.Nishi, Y.Nogi, K.Uchimura, T.Kobayashi, J.Hitomi, K.Ozaki, S.Kawai, S.Ito, and K.Horikoshi (2007).
Intragenomic diversity of the V1 regions of 16S rRNA genes in high-alkaline protease-producing Bacillus clausii spp.
  Extremophiles, 11, 597-603.  
16825361 J.Xie, B.Foxman, L.Zhang, and C.F.Marrs (2006).
Molecular epidemiologic identification of Escherichia coli genes that are potentially involved in movement of the organism from the intestinal tract to the vagina and bladder.
  J Clin Microbiol, 44, 2434-2441.  
16823601 Y.Oguchi, H.Maeda, K.Abe, T.Nakajima, T.Uchida, and Y.Yamagata (2006).
Hydrophobic interactions between the secondary structures on the molecular surface reinforce the alkaline stability of serine protease.
  Biotechnol Lett, 28, 1383-1391.  
15608117 A.P.Dubnovitsky, E.G.Kapetaniou, and A.C.Papageorgiou (2005).
Enzyme adaptation to alkaline pH: atomic resolution (1.08 A) structure of phosphoserine aminotransferase from Bacillus alcalophilus.
  Protein Sci, 14, 97.
PDB codes: 1w23 1w3u
15272186 M.Akita, N.Takeda, K.Hirasawa, H.Sakai, M.Kawamoto, M.Yamamoto, W.D.Grant, Y.Hatada, S.Ito, and K.Horikoshi (2004).
Crystallization and preliminary X-ray study of alkaline mannanase from an alkaliphilic Bacillus isolate.
  Acta Crystallogr D Biol Crystallogr, 60, 1490-1492.
PDB code: 1wky
  11556766 E.A.Zambrano, I.Rodríguez, M.Mendoza, C.Santaella, M.López, and M.Albornoz (2001).
Regulation of serine-type exoproteinases by endogenous inhibitors present in exoantigens of the mycelial form of Paracoccidioides brasiliensis.
  Med Mycol, 39, 359-368.  
11440153 H.Maeda, Y.Yamagata, E.Ichishima, and T.Nakajima (2001).
Identification of N-terminal autodigestion target site in subtilisin ALP I.
  Biosci Biotechnol Biochem, 65, 1255-1257.  
11717490 M.Akita, A.Suzuki, T.Kobayashi, S.Ito, and T.Yamane (2001).
The first structure of pectate lyase belonging to polysaccharide lyase family 3.
  Acta Crystallogr D Biol Crystallogr, 57, 1786-1792.
PDB code: 1ee6
11166997 Y.Hakamada, Y.Hatada, T.Ozawa, K.Ozaki, T.Kobayashi, and S.Ito (2001).
Identification of thermostabilizing residues in a Bacillus alkaline cellulase by construction of chimeras from mesophilic and thermostable enzymes and site-directed mutagenesis.
  FEMS Microbiol Lett, 195, 67-72.  
  10585964 K.Horikoshi (1999).
Alkaliphiles: some applications of their products for biotechnology.
  Microbiol Mol Biol Rev, 63, 735.  
10089328 T.Yamane, H.Tasaki, F.Matsumoto, A.Suzuki, N.Uozumi, and T.Ashida (1999).
Crystallization and preliminary x-ray analysis of beta-amylase from Bacillus polymyxa.
  Acta Crystallogr D Biol Crystallogr, 55, 898-900.  
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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