spacer
spacer

PDBsum entry 1up0

Go to PDB code: 
protein ligands links
Hydrolase PDB id
1up0
Jmol
Contents
Protein chain
293 a.a. *
Ligands
BGC-BGC
SO4
ACT
1PG
Waters ×317
* Residue conservation analysis
PDB id:
1up0
Name: Hydrolase
Title: Structure of the endoglucanase cel6 from mycobacterium tuberculosis in complex with cellobiose at 1.75 angstrom
Structure: Putative cellulase cel6. Chain: a. Fragment: catalytic domain, residues 88-380. Synonym: endoglucanase, cela. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: synthetic gene
Resolution:
1.75Å     R-factor:   0.144     R-free:   0.181
Authors: A.Varrot,S.Leydier,G.Pell,H.J.Gilbert,G.J.Davies
Key ref:
A.Varrot et al. (2005). Mycobacterium tuberculosis strains possess functional cellulases. J Biol Chem, 280, 20181-20184. PubMed id: 15824123 DOI: 10.1074/jbc.C500142200
Date:
26-Sep-03     Release date:   18-Nov-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q79G13  (Q79G13_MYCTU) -  Cellulase CelA1
Seq:
Struc:
380 a.a.
293 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cellulose catabolic process   1 term 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     1 term  

 

 
DOI no: 10.1074/jbc.C500142200 J Biol Chem 280:20181-20184 (2005)
PubMed id: 15824123  
 
 
Mycobacterium tuberculosis strains possess functional cellulases.
A.Varrot, S.Leydier, G.Pell, J.M.Macdonald, R.V.Stick, B.Henrissat, H.J.Gilbert, G.J.Davies.
 
  ABSTRACT  
 
The genomes of various Mycobacterium tuberculosis strains encode proteins that do not appear to play a role in the growth or survival of the bacterium in its mammalian host, including some implicated in plant cell wall breakdown. Here we show that M. tuberculosis H37Rv does indeed possess a functional cellulase. The x-ray crystal structure of this enzyme, in ligand complex forms, from 1.9 to 1.1A resolution, reveals a highly conserved substrate-binding cleft, which affords similar, and unusual, distortion of the substrate at the catalytic center. The endoglucanase activity, together with the existence of a putative membrane-associated crystalline polysaccharide-binding protein, may reflect the ancestral soil origin of the Mycobacterium or hint at a previously unconsidered environmental niche.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Oligosaccharides used in the structure determination of the M. tuberculosis Cel6. Compound 1 thio-cellopentaoside (20) (SDP5) and compound 2 a cellobio-derived isofagamine (21) are shown.
Figure 3.
FIG. 3. A schematic diagram of the interactions of M. tuberculosis Cel6 with the cellobio-derived isofagomine. Dashed lines indicate direct (i.e. non-water-mediated) interactions <2.9 Å. A key water molecule discussed in the text is shown as a shaded sphere.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 20181-20184) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21273341 D.W.Cockburn, and A.J.Clarke (2011).
Modulating the pH-activity profile of cellulase A from Cellulomonas fimi by replacement of surface residues.
  Protein Eng Des Sel, 24, 429-437.  
20150238 F.Mba Medie, I.Ben Salah, M.Drancourt, and B.Henrissat (2010).
Paradoxical conservation of a set of three cellulose-targeting genes in Mycobacterium tuberculosis complex organisms.
  Microbiology, 156, 1468-1475.  
19523117 T.V.Vuong, and D.B.Wilson (2009).
The absence of an identifiable single catalytic base residue in Thermobifida fusca exocellulase Cel6B.
  FEBS J, 276, 3837-3845.  
19734341 T.V.Vuong, and D.B.Wilson (2009).
Processivity, synergism, and substrate specificity of Thermobifida fusca Cel6B.
  Appl Environ Microbiol, 75, 6655-6661.  
  19194005 Y.Kurakata, T.Tonozuka, Y.Liu, S.Kaneko, A.Nishikawa, K.Fukuda, and M.Yoshida (2009).
Heterologous expression, crystallization and preliminary X-ray characterization of CcCel6C, a glycoside hydrolase family 6 enzyme from the basidiomycete Coprinopsis cinerea.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 140-143.  
18292875 V.A.Money, A.Cartmell, C.I.Guerreiro, V.M.Ducros, C.M.Fontes, H.J.Gilbert, and G.J.Davies (2008).
Probing the beta-1,3:1,4 glucanase, CtLic26A, with a thio-oligosaccharide and enzyme variants.
  Org Biomol Chem, 6, 851-853.
PDB code: 2vi0
17724729 B.Mertz, A.D.Hill, C.Mulakala, and P.J.Reilly (2007).
Automated docking to explore subsite binding by glycoside hydrolase family 6 cellobiohydrolases and endoglucanases.
  Biopolymers, 87, 249-260.  
17256117 R.Child, C.D.Miller, Y.Liang, G.Narasimham, J.Chatterton, P.Harrison, R.C.Sims, D.Britt, and A.J.Anderson (2007).
Polycyclic aromatic hydrocarbon-degrading Mycobacterium isolates: their association with plant roots.
  Appl Microbiol Biotechnol, 75, 655-663.  
16823793 V.A.Money, N.L.Smith, A.Scaffidi, R.V.Stick, H.J.Gilbert, and G.J.Davies (2006).
Substrate distortion by a lichenase highlights the different conformational itineraries harnessed by related glycoside hydrolases.
  Angew Chem Int Ed Engl, 45, 5136-5140.
PDB codes: 2cip 2cit
16086389 B.Mertz, R.S.Kuczenski, R.T.Larsen, A.D.Hill, and P.J.Reilly (2005).
Phylogenetic analysis of family 6 glycoside hydrolases.
  Biopolymers, 79, 197-206.  
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.