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PDBsum entry 2tbs
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Hydrolase(serine proteinase) PDB id
2tbs

 

 

 

 

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Contents
Protein chain
222 a.a. *
Ligands
BEN
Metals
_CA
Waters ×164
* Residue conservation analysis
PDB id:
2tbs
Name: Hydrolase(serine proteinase)
Title: Cold-adaption of enzymes: structural comparison between salmon and bovine trypsins
Structure: Trypsin. Chain: a. Engineered: yes
Source: Salmo salar. Atlantic salmon. Organism_taxid: 8030
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   not given    
Authors: A.O.Smalas
Key ref: A.O.Smalås et al. (1994). Cold adaption of enzymes: structural comparison between salmon and bovine trypsins. Proteins, 20, 149-166. PubMed id: 7846025
Date:
14-Jan-94     Release date:   30-Apr-94    
Supersedes: 1tbs
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P35031  (TRY1_SALSA) -  Trypsin-1 from Salmo salar
Seq:
Struc: 		242 a.a.
222 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.4  - trypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.

 

 
Proteins 20:149-166 (1994)
PubMed id: 7846025  
 
 
Cold adaption of enzymes: structural comparison between salmon and bovine trypsins.
A.O.Smalås, E.S.Heimstad, A.Hordvik, N.P.Willassen, R.Male.
 
  ABSTRACT  
 
The crystal structure of an anionic form of salmon trypsin has been determined at 1.82 A resolution. We report the first structure of a trypsin from a phoikilothermic organism in a detailed comparison to mammalian trypsins in order to look for structural rationalizations for the cold-adaption features of salmon trypsin. This form of salmon trypsin (ST II) comprises 222 residues, and is homologous to bovine trypsin (BT) in about 65% of the primary structure. The tertiary structures are similar, with an overall displacement in main chain atomic positions between salmon trypsin and various crystal structures of bovine trypsin of about 0.8 A. Intramolecular hydrogen bonds and hydrophobic interactions are compared and discussed in order to estimate possible differences in molecular flexibility which might explain the higher catalytic efficiency and lower thermostability of salmon trypsin compared to bovine trypsin. No overall differences in intramolecular interactions are detected between the two structures, but there are differences in certain regions of the structures which may explain some of the observed differences in physical properties. The distribution of charged residues is different in the two trypsins, and the impact this might have on substrate affinity has been discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20057143 H.Tsuruta, B.Mikami, T.Higashi, and Y.Aizono (2010).
Crystal structure of cold-active alkaline phosphatase from the psychrophile Shewanella sp.
  Biosci Biotechnol Biochem, 74, 69-74.
PDB code: 3a52
20169386 L.Rojo, A.Muhlia-Almazan, R.Saborowski, and F.García-Carreño (2010).
Aspartic cathepsin D endopeptidase contributes to extracellular digestion in clawed lobsters Homarus americanus and Homarus gammarus.
  Mar Biotechnol (NY), 12, 696-707.  
19564692 E.Toyota, D.Iyaguchi, H.Sekizaki, M.Tateyama, and K.K.Ng (2009).
A structural comparison of three isoforms of anionic trypsin from chum salmon (Oncorhynchus keta).
  Acta Crystallogr D Biol Crystallogr, 65, 717-723.
PDB codes: 2zpq 2zpr 2zps
19759914 S.González, M.Fló, M.Margenat, R.Durán, G.González-Sapienza, M.Graña, J.Parkinson, R.M.Maizels, G.Salinas, B.Alvarez, and C.Fernández (2009).
A family of diverse Kunitz inhibitors from Echinococcus granulosus potentially involved in host-parasite cross-talk.
  PLoS One, 4, e7009.  
18695720 A.I.Papisova, S.A.Semenova, I.u.A.Kislitsyn, and G.N.Rudenskaia (2008).
[Characteristics of substrate hydrolysis by endopeptidases from the hepatopancreas of the king crab]
  Bioorg Khim, 34, 479-486.  
18404270 A.Muhlia-Almazán, A.Sánchez-Paz, and F.L.García-Carreño (2008).
Invertebrate trypsins: a review.
  J Comp Physiol [B], 178, 655-672.  
18196298 M.Olufsen, A.O.Smalås, and B.O.Brandsdal (2008).
Electrostatic interactions play an essential role in DNA repair and cold-adaptation of Uracil DNA glycosylase.
  J Mol Model, 14, 201-213.  
17310272 S.Srimathi, G.Jayaraman, G.Feller, B.Danielsson, and P.R.Narayanan (2007).
Intrinsic halotolerance of the psychrophilic alpha-amylase from Pseudoalteromonas haloplanktis.
  Extremophiles, 11, 505-515.  
16756497 K.S.Siddiqui, and R.Cavicchioli (2006).
Cold-adapted enzymes.
  Annu Rev Biochem, 75, 403-433.  
16294337 O.A.Adekoya, R.Helland, N.P.Willassen, and I.Sylte (2006).
Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family.
  Proteins, 62, 435-449.  
15759084 A.Gudmundsdóttir, and H.M.Pálsdóttir (2005).
Atlantic cod trypsins: from basic research to practical applications.
  Mar Biotechnol (NY), 7, 77-88.  
15670163 J.Arnórsdóttir, M.M.Kristjánsson, and R.Ficner (2005).
Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation.
  FEBS J, 272, 832-845.
PDB codes: 1s2n 1sh7
  16233714 A.Hoyoux, V.Blaise, T.Collins, S.D'Amico, E.Gratia, A.L.Huston, J.C.Marx, G.Sonan, Y.Zeng, G.Feller, and C.Gerday (2004).
Extreme catalysts from low-temperature environments.
  J Biosci Bioeng, 98, 317-330.  
14975528 D.Georlette, V.Blaise, T.Collins, S.D'Amico, E.Gratia, A.Hoyoux, J.C.Marx, G.Sonan, G.Feller, and C.Gerday (2004).
Some like it cold: biocatalysis at low temperatures.
  FEMS Microbiol Rev, 28, 25-42.  
15100224 E.Bae, and G.N.Phillips (2004).
Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases.
  J Biol Chem, 279, 28202-28208.
PDB codes: 1p3j 1s3g
15044735 H.K.Leiros, B.O.Brandsdal, O.A.Andersen, V.Os, I.Leiros, R.Helland, J.Otlewski, N.P.Willassen, and A.O.Smalås (2004).
Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements.
  Protein Sci, 13, 1056-1070.
PDB codes: 1utj 1utk 1utl 1utm 1utn 1uto 1utp 1utq
12475991 F.Van Petegem, T.Collins, M.A.Meuwis, C.Gerday, G.Feller, and J.Van Beeumen (2003).
The structure of a cold-adapted family 8 xylanase at 1.3 A resolution. Structural adaptations to cold and investgation of the active site.
  J Biol Chem, 278, 7531-7539.
PDB codes: 1h12 1h13 1h14
15035024 G.Feller, and C.Gerday (2003).
Psychrophilic enzymes: hot topics in cold adaptation.
  Nat Rev Microbiol, 1, 200-208.  
12876336 I.Leiros, E.Moe, O.Lanes, A.O.Smalås, and N.P.Willassen (2003).
The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features.
  Acta Crystallogr D Biol Crystallogr, 59, 1357-1365.
PDB code: 1okb
12577270 N.Aghajari, F.Van Petegem, V.Villeret, J.P.Chessa, C.Gerday, R.Haser, and J.Van Beeumen (2003).
Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases.
  Proteins, 50, 636-647.
PDB codes: 1g9k 1h71
12437096 A.Gudmundsdóttir (2002).
Cold-adapted and mesophilic brachyurins.
  Biol Chem, 383, 1125-1131.  
11784309 A.Lönn, M.Gárdonyi, W.van Zyl, B.Hahn-Hägerdal, and R.C.Otero (2002).
Cold adaptation of xylose isomerase from Thermus thermophilus through random PCR mutagenesis. Gene cloning and protein characterization.
  Eur J Biochem, 269, 157-163.  
11933070 G.Gianese, F.Bossa, and S.Pascarella (2002).
Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes.
  Proteins, 47, 236-249.  
11121112 D.C.Benjamin, S.Kristjánsdóttir, and A.Gudmundsdóttir (2001).
Increasing the thermal stability of euphauserase. A cold-active and multifunctional serine protease from Antarctic krill.
  Eur J Biochem, 268, 127-131.  
11264577 H.K.Leiros, S.M.McSweeney, and A.O.Smalås (2001).
Atomic resolution structures of trypsin provide insight into structural radiation damage.
  Acta Crystallogr D Biol Crystallogr, 57, 488-497.
PDB codes: 1hj8 1hj9
11470375 J.A.Irwin, G.A.Alfredsson, A.J.Lanzetti, H.M.Gudmundsson, and P.C.Engel (2001).
Purification and characterisation of a serine peptidase from the marine psychrophile strain PA-43.
  FEMS Microbiol Lett, 201, 285-290.  
10842337 A.A.Gorfe, B.O.Brandsdal, H.K.Leiros, R.Helland, and A.O.Smalås (2000).
Electrostatics of mesophilic and psychrophilic trypsin isoenzymes: qualitative evaluation of electrostatic differences at the substrate binding site.
  Proteins, 40, 207-217.  
10848966 D.Georlette, Z.O.Jónsson, F.Van Petegem, J.Chessa, J.Van Beeumen, U.Hübscher, and C.Gerday (2000).
A DNA ligase from the psychrophile Pseudoalteromonas haloplanktis gives insights into the adaptation of proteins to low temperatures.
  Eur J Biochem, 267, 3502-3512.  
10672012 H.K.Leiros, N.P.Willassen, and A.O.Smalås (2000).
Structural comparison of psychrophilic and mesophilic trypsins. Elucidating the molecular basis of cold-adaptation.
  Eur J Biochem, 267, 1039-1049.  
11087937 M.A.Ciardiello, L.Camardella, V.Carratore, and G.di Prisco (2000).
L-Glutamate dehydrogenase from the antarctic fish Chaenocephalus aceratus. Primary structure, function and thermodynamic characterisation: relationship with cold adaptation.
  Biochim Biophys Acta, 1543, 11-23.  
10601858 R.Di Fraia, V.Wilquet, M.A.Ciardiello, V.Carratore, A.Antignani, L.Camardella, N.Glansdorff, and G.Di Prisco (2000).
NADP+-dependent glutamate dehydrogenase in the Antarctic psychrotolerant bacterium Psychrobacter sp. TAD1. Characterization, protein and DNA sequence, and relationship to other glutamate dehydrogenases.
  Eur J Biochem, 267, 121-131.  
11011764 R.Spilliaert, and A.Gudmundsdóttir (2000).
Molecular cloning of the Atlantic cod chymotrypsinogen B.
  Microb Comp Genomics, 5, 41-50.  
11087936 T.Lonhienne, C.Gerday, and G.Feller (2000).
Psychrophilic enzymes: revisiting the thermodynamic parameters of activation may explain local flexibility.
  Biochim Biophys Acta, 1543, 1.  
10089404 R.Helland, G.I.Berglund, J.Otlewski, W.Apostoluk, O.A.Andersen, N.P.Willassen, and A.O.Smalås (1999).
High-resolution structures of three new trypsin-squash-inhibitor complexes: a detailed comparison with other trypsins and their complexes.
  Acta Crystallogr D Biol Crystallogr, 55, 139-148.
PDB codes: 2btc 2sta 2stb
9682487 K.Sun, L.Camardella, G.Di Prisco, and G.Hervé (1998).
Properties of aspartate transcarbamylase from TAD1, a psychrophilic bacterial strain isolated from Antarctica.
  FEMS Microbiol Lett, 164, 375-382.  
9551556 R.J.Russell, U.Gerike, M.J.Danson, D.W.Hough, and G.L.Taylor (1998).
Structural adaptations of the cold-active citrate synthase from an Antarctic bacterium.
  Structure, 6, 351-361.
PDB code: 1a59
7556223 R.Male, J.B.Lorens, A.O.Smalås, and K.R.Torrissen (1995).
Molecular cloning and characterization of anionic and cationic variants of trypsin from Atlantic salmon.
  Eur J Biochem, 232, 677-685.  
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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