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PDBsum entry 1g01

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protein ligands metals links
Hydrolase PDB id
1g01
Jmol
Contents
Protein chain
357 a.a. *
Ligands
ACY ×5
Metals
_CD ×10
Waters ×465
* Residue conservation analysis
PDB id:
1g01
Name: Hydrolase
Title: Alkaline cellulase k catalytic domain
Structure: Endoglucanase. Chain: a. Fragment: alkaline cellulase k catalytic domain. Engineered: yes
Source: Bacillus sp.. Organism_taxid: 1415. Strain: ksm-635. Expressed in: bacillus subtilis. Expression_system_taxid: 1423.
Resolution:
1.90Å     R-factor:   0.196     R-free:   0.227
Authors: T.Shirai,H.Ishida,J.Noda,T.Yamane,K.Ozaki,Y.Hakamada,S.Ito
Key ref:
T.Shirai et al. (2001). Crystal structure of alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme. J Mol Biol, 310, 1079-1087. PubMed id: 11501997 DOI: 10.1006/jmbi.2001.4835
Date:
05-Oct-00     Release date:   01-Aug-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P19424  (GUN_BACS6) -  Endoglucanase
Seq:
Struc:
 
Seq:
Struc:
941 a.a.
357 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.4  - Cellulase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     2 terms  

 

 
DOI no: 10.1006/jmbi.2001.4835 J Mol Biol 310:1079-1087 (2001)
PubMed id: 11501997  
 
 
Crystal structure of alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme.
T.Shirai, H.Ishida, J.Noda, T.Yamane, K.Ozaki, Y.Hakamada, S.Ito.
 
  ABSTRACT  
 
The crystal structure of the catalytic domain of alkaline cellulase K was determined at 1.9 A resolution. Because of the most alkaliphilic nature and it's highest activity at pH 9.5, it is used commercially in laundry detergents. An analysis of the structural bases of the alkaliphilic character of the enzyme suggested a mechanism similar to that previously proposed for alkaline proteases, that is, an increase in the number of Arg, His, and Gln residues, and a decrease in Asp and Lys residues. Some ion pairs were formed by the gained Arg residues, which is similar to what has been found in the alkaline proteases. Lys-Asp ion pairs are disfavored and partly replaced with Arg-Asp ion pairs. The alkaline adaptation appeared to be a remodeling of ion pairs so that the charge balance is kept in the high pH range.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. (a) The active center structure of the CelK-cellobiose complex. Side-chains of the active site residues are shown in orange. The red sphere is the cadmium ion found at the catalytic site. Hydrogen bonds are shown in yellow. The cellobiose molecule is shown in green. F[o] -F[c] electron density map is superimposed to the model (contoured at 2.5s level, the atoms of cellobiose were excluded from the phase calculation). (b) The active center and carbohydrate ligand structures of CelK and Cel5A in different ligand states. Only the main-chain atoms are presented for the loops Ala233-Gly239 of Cel5A and Gln490-Gly495 of CelK. The bound sugars are labeled according to the binding sites. Hydrogen bonds are shown in yellow. The superimposed structures are Cel5A without ligand (open conformation, green), complexed with cellobiose (open conformation, blue) and covalent-intermediate (closed conformation, gray) and CelK without ligand (closed conformation, red) and cellobiose complex (closed conformation, orange).
Figure 5.
Figure 5. Spatial distribution of the acquired Arg and His residues (red) and eliminated Lys residues (gray) that appeared to be responsible for the ion pair remodeling. Shown in blue are the negatively charged residues that might form an ion pair with the Arg, His or Lys residues. The cellobiose molecule is shown in green. Hydrogen bonds are shown in yellow.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 310, 1079-1087) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20803139 C.Liang, Y.Xue, M.Fioroni, F.Rodríguez-Ropero, C.Zhou, U.Schwaneberg, and Y.Ma (2011).
Cloning and characterization of a thermostable and halo-tolerant endoglucanase from Thermoanaerobacter tengcongensis MB4.
  Appl Microbiol Biotechnol, 89, 315-326.  
17021659 L.Redecke, M.A.Brehm, and R.Bredehorst (2007).
Cloning and characterization of dihydrofolate reductase from a facultative alkaliphilic and halotolerant bacillus strain.
  Extremophiles, 11, 75-83.  
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
16240096 E.Papaleo, P.Fantucci, M.Vai, and L.De Gioia (2006).
Three-dimensional structure of the catalytic domain of the yeast beta-(1,3)-glucan transferase Gas1: a molecular modeling investigation.
  J Mol Model, 12, 237-248.  
16696704 J.C.Voorhees, J.P.Ferrance, and J.P.Landers (2006).
Enhanced elution of sperm from cotton swabs via enzymatic digestion for rape kit analysis.
  J Forensic Sci, 51, 574-579.  
16710633 K.Hirasawa, K.Uchimura, M.Kashiwa, W.D.Grant, S.Ito, T.Kobayashi, and K.Horikoshi (2006).
Salt-activated endoglucanase of a strain of alkaliphilic Bacillus agaradhaerens.
  Antonie Van Leeuwenhoek, 89, 211-219.  
16823036 K.Manikandan, A.Bhardwaj, N.Gupta, N.K.Lokanath, A.Ghosh, V.S.Reddy, and S.Ramakumar (2006).
Crystal structures of native and xylosaccharide-bound alkali thermostable xylanase from an alkalophilic Bacillus sp. NG-27: structural insights into alkalophilicity and implications for adaptation to polyextreme conditions.
  Protein Sci, 15, 1951-1960.
PDB codes: 2f8q 2fgl
16142468 Y.H.Li, M.Ding, J.Wang, G.J.Xu, and F.Zhao (2006).
A novel thermoacidophilic endoglucanase, Ba-EGA, from a new cellulose-degrading bacterium, Bacillus sp.AC-1.
  Appl Microbiol Biotechnol, 70, 430-436.  
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
15857788 T.Wang, X.Liu, Q.Yu, X.Zhang, Y.Qu, P.Gao, and T.Wang (2005).
Directed evolution for engineering pH profile of endoglucanase III from Trichoderma reesei.
  Biomol Eng, 22, 89-94.  
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
12761390 J.Le Nours, C.Ryttersgaard, L.Lo Leggio, P.R.Østergaard, T.V.Borchert, L.L.Christensen, and S.Larsen (2003).
Structure of two fungal beta-1,4-galactanases: searching for the basis for temperature and pH optimum.
  Protein Sci, 12, 1195-1204.
PDB codes: 1hjq 1hjs 1hju
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.