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PDBsum entry 1tvp

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1tvp
Jmol PyMol
Contents
Protein chains
293 a.a. *
Ligands
EPE
CBI
Waters ×698
* Residue conservation analysis
PDB id:
1tvp
Name: Hydrolase
Title: Endoglucanase cel5g from pseudoalteromonas haloplanktis in complex with cellobiose
Structure: Cellulase. Chain: a, b. Fragment: catalytic domain. Synonym: endoglucanase g. Engineered: yes
Source: Pseudoalteromonas haloplanktis. Organism_taxid: 228. Gene: celg. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.60Å     R-factor:   0.158     R-free:   0.189
Authors: S.Violot,R.Haser,N.Aghajari
Key ref:
S.Violot et al. (2005). Structure of a full length psychrophilic cellulase from Pseudoalteromonas haloplanktis revealed by X-ray diffraction and small angle X-ray scattering. J Mol Biol, 348, 1211-1224. PubMed id: 15854656 DOI: 10.1016/j.jmb.2005.03.026
Date:
30-Jun-04     Release date:   17-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O86099  (O86099_PSEHA) -  Cellulase
Seq:
Struc:
494 a.a.
293 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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   1 term 
  Biochemical function     hydrolase activity, hydrolyzing O-glycosyl compounds     1 term  

 

 
DOI no: 10.1016/j.jmb.2005.03.026 J Mol Biol 348:1211-1224 (2005)
PubMed id: 15854656  
 
 
Structure of a full length psychrophilic cellulase from Pseudoalteromonas haloplanktis revealed by X-ray diffraction and small angle X-ray scattering.
S.Violot, N.Aghajari, M.Czjzek, G.Feller, G.K.Sonan, P.Gouet, C.Gerday, R.Haser, V.Receveur-Bréchot.
 
  ABSTRACT  
 
Pseudoalteromonas haloplanktis is a psychrophilic Gram-negative bacterium isolated in Antarctica, that lives on organic remains of algae. This bacterium converts the cellulose, highly constitutive of algae, into an immediate nutritive form by biodegrading this biopolymer. To understand the mechanisms of cold adaptation of its enzymatic components, we studied the structural properties of an endoglucanase, Cel5G, by complementary methods, X-ray crystallography and small angle X-ray scattering. Using X-ray crystallography, we determined the structure of the catalytic core module of this family 5 endoglucanase, at 1.4A resolution in its native form and at 1.6A in the cellobiose-bound form. The catalytic module of Cel5G presents the (beta/alpha)(8)-barrel structure typical of clan GH-A of glycoside hydrolase families. The structural comparison of the catalytic core of Cel5G with the mesophilic catalytic core of Cel5A from Erwinia chrysanthemi revealed modifications at the atomic level leading to higher flexibility and thermolability, which might account for the higher activity of Cel5G at low temperatures. Using small angle X-ray scattering we further explored the structure at the entire enzyme level. We analyzed the dimensions, shape, and conformation of Cel5G full length in solution and especially of the linker between the catalytic module and the cellulose-binding module. The results showed that the linker is unstructured, and unusually long and flexible, a peculiarity that distinguishes it from its mesophilic counterpart. Loops formed at the base by disulfide bridges presumably add constraints to stabilize the most extended conformations. These results suggest that the linker plays a major role in cold adaptation of this psychrophilic enzyme, allowing steric optimization of substrate accessibility.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (a) Stereo view of the superimposition of the catalytic module of Cel5G (blue) on that of Cel5A from E. chrysanthemi (red) catalytic module. The Figure was prepared with MOLSCRIPT60 and BOBSCRIPT.61^ and 62 (b) Sequence comparison of the catalytic modules of Cel5G (blue) with Cel5A E. chrysanthemi (red), respectively. Catalytic residues are indicated (blue font), as well as supplementary residues in Cel5G[CM] versus Cel5A[CM] (golden font). The eight conserved residues in family 5 are indicated (green stars), as well as the three conserved residues in subfamily 5-2 (pink stars). Sequence alignment was performed with the program CLUSTAL62 and color coded with ESPript.63
Figure 6.
Figure 6. (a) Shape calculated with GASBOR (blue) superimposed with ten different models of Cel5G provided by GLOOPY represented by secondary structure element type. (b) C^a trace of a typical linker modelled by GLOOPY exhibiting loops (red) putatively closed by disulfide bonds (yellow). (c) Fit on the experimental scattering curve obtained with the average form factor of the different models provided by GLOOPY.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 348, 1211-1224) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20511418 W.Liu, X.Z.Zhang, Z.Zhang, and Y.H.Zhang (2010).
Engineering of Clostridium phytofermentans Endoglucanase Cel5A for improved thermostability.
  Appl Environ Microbiol, 76, 4914-4917.  
19617364 B.J.Watson, H.Zhang, A.G.Longmire, Y.H.Moon, and S.W.Hutcheson (2009).
Processive endoglucanases mediate degradation of cellulose by Saccharophagus degradans.
  J Bacteriol, 191, 5697-5705.  
  19255469 B.Zheng, W.Yang, Y.Wang, Y.Feng, and Z.Lou (2009).
Crystallization and preliminary crystallographic analysis of thermophilic cellulase from Fervidobacterium nodosum Rt17-B1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 219-222.  
19162471 D.Eliezer (2009).
Biophysical characterization of intrinsically disordered proteins.
  Curr Opin Struct Biol, 19, 23-30.  
18539590 C.Bauvois, L.Jacquamet, A.L.Huston, F.Borel, G.Feller, and J.L.Ferrer (2008).
Crystal structure of the cold-active aminopeptidase from Colwellia psychrerythraea, a close structural homologue of the human bifunctional leukotriene A4 hydrolase.
  J Biol Chem, 283, 23315-23325.
PDB code: 3cia
18312599 C.Michaux, J.Massant, F.Kerff, J.M.Frère, J.D.Docquier, I.Vandenberghe, B.Samyn, A.Pierrard, G.Feller, P.Charlier, J.Van Beeumen, and J.Wouters (2008).
Crystal structure of a cold-adapted class C beta-lactamase.
  FEBS J, 275, 1687-1697.
PDB code: 2qz6
18368288 E.Stefanidi, and C.E.Vorgias (2008).
Molecular analysis of the gene encoding a new chitinase from the marine psychrophilic bacterium Moritella marina and biochemical characterization of the recombinant enzyme.
  Extremophiles, 12, 541-552.  
18755688 Y.Zhang, J.Ju, H.Peng, F.Gao, C.Zhou, Y.Zeng, Y.Xue, Y.Li, B.Henrissat, G.F.Gao, and Y.Ma (2008).
Biochemical and Structural Characterization of the Intracellular Mannanase AaManA of Alicyclobacillus acidocaldarius Reveals a Novel Glycoside Hydrolase Family Belonging to Clan GH-A.
  J Biol Chem, 283, 31551-31558.
PDB code: 3civ
17513582 D.Flament, T.Barbeyron, M.Jam, P.Potin, M.Czjzek, B.Kloareg, and G.Michel (2007).
Alpha-agarases define a new family of glycoside hydrolases, distinct from beta-agarase families.
  Appl Environ Microbiol, 73, 4691-4694.  
17121820 D.K.Poon, S.G.Withers, and L.P.McIntosh (2007).
Direct demonstration of the flexibility of the glycosylated proline-threonine linker in the Cellulomonas fimi Xylanase Cex through NMR spectroscopic analysis.
  J Biol Chem, 282, 2091-2100.  
17937912 G.Rosenblum, P.E.Van den Steen, S.R.Cohen, J.G.Grossmann, J.Frenkel, R.Sertchook, N.Slack, R.W.Strange, G.Opdenakker, and I.Sagi (2007).
Insights into the structure and domain flexibility of full-length pro-matrix metalloproteinase-9/gelatinase B.
  Structure, 15, 1227-1236.  
17391014 H.Xie, S.Vucetic, L.M.Iakoucheva, C.J.Oldfield, A.K.Dunker, V.N.Uversky, and Z.Obradovic (2007).
Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions.
  J Proteome Res, 6, 1882-1898.  
17766385 R.A.Goldstein (2007).
Amino-acid interactions in psychrophiles, mesophiles, thermophiles, and hyperthermophiles: insights from the quasi-chemical approximation.
  Protein Sci, 16, 1887-1895.  
16705665 K.S.Siddiqui, A.Poljak, M.Guilhaus, D.De Francisci, P.M.Curmi, G.Feller, S.D'Amico, C.Gerday, V.N.Uversky, and R.Cavicchioli (2006).
Role of lysine versus arginine in enzyme cold-adaptation: modifying lysine to homo-arginine stabilizes the cold-adapted alpha-amylase from Pseudoalteramonas haloplanktis.
  Proteins, 64, 486-501.  
16756497 K.S.Siddiqui, and R.Cavicchioli (2006).
Cold-adapted enzymes.
  Annu Rev Biochem, 75, 403-433.  
16585939 S.D'Amico, T.Collins, J.C.Marx, G.Feller, and C.Gerday (2006).
Psychrophilic microorganisms: challenges for life.
  EMBO Rep, 7, 385-389.  
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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