PDBsum entry 1g9k

Go to PDB code: 
protein ligands metals links
Hydrolase PDB id
Protein chain
455 a.a. *
_CA ×7
Waters ×355
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of a psychrophilic alkaline protease from pseudomonas tac ii 18
Structure: Serralysin. Chain: a. Synonym: calcium and zinc dependent alkaline protease. Ec:
Source: Pseudomonas. Organism_taxid: 286. Strain: tac ii 18
Biol. unit: Trimer (from PQS)
1.96Å     R-factor:   0.156     R-free:   0.187
Authors: N.Aghajari,R.Haser
Key ref:
N.Aghajari et al. (2003). Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases. Proteins, 50, 636-647. PubMed id: 12577270 DOI: 10.1002/prot.10264
24-Nov-00     Release date:   14-Feb-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O69771  (O69771_9PSED) -  Serralysin
480 a.a.
455 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Serralysin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage of bonds with hydrophobic residues in P1'.
      Cofactor: Zn(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular space   2 terms 
  Biological process     proteolysis   1 term 
  Biochemical function     hydrolase activity     6 terms  


DOI no: 10.1002/prot.10264 Proteins 50:636-647 (2003)
PubMed id: 12577270  
Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases.
N.Aghajari, F.Van Petegem, V.Villeret, J.P.Chessa, C.Gerday, R.Haser, J.Van Beeumen.
Enzymes from psychrophilic organisms differ from their mesophilic counterparts in having a lower thermostability and a higher specific activity at low and moderate temperatures. It is in general accepted that psychrophilic enzymes are more flexible to allow easy accommodation and transformation of the substrates at low energy costs. Here, we report the structures of two crystal forms of the alkaline protease from an Antarctic Pseudomonas species (PAP), solved to 2.1- and 1.96-A resolution, respectively. Comparative studies of PAP structures with mesophilic counterparts show that the overall structures are similar but that the conformation of the substrate-free active site in PAP resembles that of the substrate-bound region of the mesophilic homolog, with both an active-site tyrosine and a substrate-binding loop displaying a conformation as in the substrate-bound form of the mesophilic proteases. Further, a region in the catalytic domain of PAP undergoes a conformational change with a loop movement as large as 13 A, induced by the binding of an extra calcium ion. Finally, the active site is more accessible due to deletions occurring in surrounding loop regions.
  Selected figure(s)  
Figure 2.
Figure 2. (a) General overview of the structure of PAP. The N-terminal (catalytic) domain is blue and the C-terminal domain red. Calcium ions in the C-terminal domain are indicated as yellow spheres, the extra calcium in the N-terminal domain is purple, and the Zn ion green. A sulphate ion (only present in form 2) is shown in the catalytic domain as well. (b) Superposition of PAP form 1 (blue) and form 2 (cyan) with AP (red) and SMP (yellow). (a) and (b) were made using MOLSCRIPT.[45] (c) Representation of conserved regions coloured as degree of similarity with AP and serralysin (SMP), where red indicates highly conserved areas (drawing made using the program BOBSCRIPT[46]).
Figure 4.
Figure 4. (a) Zn^2+ coordination site of PAP form 1 with the Zn^2+ ion (grey sphere) coordinating three histidines (169, 173, and 179), a tyrosine (209), which has a double conformation, and a water molecule (red). (b) Superpositions of the active-site Tyr(209) and Zn^2+ of PAP (the two conformations for crystal form 1 in blue and one conformation for form 2 in green with corresponding unligated (red) and ligated (light brown) Tyr in AP.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2003, 50, 636-647) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20646925 A.Casanueva, M.Tuffin, C.Cary, and D.A.Cowan (2010).
Molecular adaptations to psychrophily: the impact of 'omic' technologies.
  Trends Microbiol, 18, 374-381.  
20530907 C.Yang, F.Wang, J.Hao, K.Zhang, N.Yuan, and M.Sun (2010).
Identification of a proteolytic bacterium, HW08, and characterization of its extracellular cold-active alkaline metalloprotease Ps5.
  Biosci Biotechnol Biochem, 74, 1220-1225.  
20047457 R.C.Kasana (2010).
Proteases from psychrotrophs: an overview.
  Crit Rev Microbiol, 36, 134-145.  
20726028 R.M.Evans, E.M.Behiry, L.H.Tey, J.Guo, E.J.Loveridge, and R.K.Allemann (2010).
Catalysis by dihydrofolate reductase from the psychropiezophile Moritella profunda.
  Chembiochem, 11, 2010-2017.  
19181663 B.B.Xie, F.Bian, X.L.Chen, H.L.He, J.Guo, X.Gao, Y.X.Zeng, B.Chen, B.C.Zhou, and Y.Z.Zhang (2009).
Cold adaptation of zinc metalloproteases in the thermolysin family from deep sea and arctic sea ice bacteria revealed by catalytic and structural properties and molecular dynamics: new insights into relationship between conformational flexibility and hydrogen bonding.
  J Biol Chem, 284, 9257-9269.  
17937401 O.Almog, A.Kogan, M.Leeuw, G.Y.Gdalevsky, R.Cohen-Luria, and A.H.Parola (2008).
Structural insights into cold inactivation of tryptophanase and cold adaptation of subtilisin S41.
  Biopolymers, 89, 354-359.  
  17329810 C.Angkawidjaja, D.J.You, H.Matsumura, Y.Koga, K.Takano, and S.Kanaya (2007).
Extracellular overproduction and preliminary crystallographic analysis of a family I.3 lipase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 187-189.  
17235516 V.Spiwok, P.Lipovová, T.Skálová, J.Dusková, J.Dohnálek, J.Hasek, N.J.Russell, and B.Králová (2007).
Cold-active enzymes studied by comparative molecular dynamics simulation.
  J Mol Model, 13, 485-497.  
16407237 F.L.Aachmann, B.I.Svanem, P.Güntert, S.B.Petersen, S.Valla, and R.Wimmer (2006).
NMR structure of the R-module: a parallel beta-roll subunit from an Azotobacter vinelandii mannuronan C-5 epimerase.
  J Biol Chem, 281, 7350-7356.
PDB code: 2agm
16756497 K.S.Siddiqui, and R.Cavicchioli (2006).
Cold-adapted enzymes.
  Annu Rev Biochem, 75, 403-433.  
15759084 A.Gudmundsdóttir, and H.M.Pálsdóttir (2005).
Atlantic cod trypsins: from basic research to practical applications.
  Mar Biotechnol (NY), 7, 77-88.  
  16511027 D.Dong, T.Ihara, H.Motoshima, and K.Watanabe (2005).
Crystallization and preliminary X-ray crystallographic studies of a psychrophilic subtilisin-like protease Apa1 from Antarctic Pseudoalteromonas sp. strain AS-11.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 308-311.  
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.  
15678758 F.J.Stevens (2004).
Amyloid formation: an emulation of matrix protein assembly?
  Amyloid, 11, 232-244.  
14765110 H.Nummelin, M.C.Merckel, J.C.Leo, H.Lankinen, M.Skurnik, and A.Goldman (2004).
The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel beta-roll.
  EMBO J, 23, 701-711.
PDB code: 1p9h
15035024 G.Feller, and C.Gerday (2003).
Psychrophilic enzymes: hot topics in cold adaptation.
  Nat Rev Microbiol, 1, 200-208.  
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.