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PDBsum entry 1ssx

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Hydrolase PDB id
1ssx
Jmol
Contents
Protein chain
198 a.a. *
Ligands
SO4 ×4
GOL ×2
Waters ×543
* Residue conservation analysis
PDB id:
1ssx
Name: Hydrolase
Title: 0.83a resolution crystal structure of alpha-lytic protease a
Structure: Alpha-lytic protease. Chain: a. Fragment: mature protease domain (residues 200-397). Synonym: alpha-lytic endopeptidase. Engineered: yes
Source: Lysobacter enzymogenes. Organism_taxid: 69. Gene: alpha-lp. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
0.83Å     R-factor:   0.087     R-free:   0.099
Authors: C.N.Fuhrmann,D.A.Agard
Key ref:
C.N.Fuhrmann et al. (2004). The 0.83 A resolution crystal structure of alpha-lytic protease reveals the detailed structure of the active site and identifies a source of conformational strain. J Mol Biol, 338, 999. PubMed id: 15111063 DOI: 10.1016/j.jmb.2004.03.018
Date:
24-Mar-04     Release date:   04-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00778  (PRLA_LYSEN) -  Alpha-lytic protease
Seq:
Struc:
397 a.a.
198 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.12  - Alpha-lytic endopeptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins, especially bonds adjacents to L-alanine and L-valine residues in bacterial cell walls, elastin and other proteins.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
DOI no: 10.1016/j.jmb.2004.03.018 J Mol Biol 338:999 (2004)
PubMed id: 15111063  
 
 
The 0.83 A resolution crystal structure of alpha-lytic protease reveals the detailed structure of the active site and identifies a source of conformational strain.
C.N.Fuhrmann, B.A.Kelch, N.Ota, D.A.Agard.
 
  ABSTRACT  
 
The crystal structure of the extracellular bacterial serine protease alpha-lytic protease (alphaLP) has been solved at 0.83 A resolution at pH 8. This ultra-high resolution structure allows accurate analysis of structural elements not possible with previous structures. Hydrogen atoms are visible, and confirm active-site hydrogen-bonding interactions expected for the apo enzyme. In particular, His57 N(delta1) participates in a normal hydrogen bond with Asp102 in the catalytic triad, with a hydrogen atom visible 0.83(+/-0.06)A from the His N(delta1). The catalytic Ser195 occupies two conformations, one corresponding to a population of His57 that is doubly protonated, the other to the singly protonated His57. Based on the occupancy of these conformations, the pKa of His57 is calculated to be approximately 8.8 when a sulfate ion occupies the active site. This 0.83 A structure has allowed critical analysis of geometric distortions within the structure. Interestingly, Phe228 is significantly distorted from planarity. The distortion of Phe228, buried in the core of the C-terminal domain, occurs at an estimated energetic cost of 4.1 kcal/mol. The conformational space for Phe228 is severely limited by the presence of Trp199, which prevents Phe228 from adopting the rotamer observed in many other chymotrypsin family members. In alphaLP, the only allowed rotamer leads to the deformation of Phe228 due to steric interactions with Thr181. We hypothesize that tight packing of co-evolved residues in this region, and the subsequent deformation of Phe228, contributes to the high cooperativity and large energetic barriers for folding and unfolding of alphaLP. The kinetic stability imparted by the large, cooperative unfolding barrier plays a critical role in extending the lifetime of the protease in its harsh environment.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. The active site. (a) Two large solvent molecules, a sulfate ion (Sul202) and a glycerol molecule (Gol210), are present near the active site. Sul202 hydrogen bonds with Ser195 and with Gly193 in the oxyanion hole, and is stabilized electrostatically by nearby Arg122 and Arg192. Gol210 occupies the S2 binding pocket of aLP, which is bordered by Tyr171, Phe94, and His57. For simplicity, 2F[o] -F[c] electron density (contoured at 2s) is shown only for Sul202 and Gol210. (b) Ser195 occupies two conformations, with only the minor conformation (Ser195[a] Og) in ideal geometry for hydrogen bonding with His57. s[A]-weighted F[o] -F[c] electron density peaks are visible at 2s (pink) for all His57 imidazole protons except N epsilon 2 (which is only partially protonated at pH 8 in the apo-enzyme). His57 Nd1 and Asp102 Od2 interact via a standard hydrogen bond. The final model is represented by sticks and water molecules are displayed as red spheres. The hydrogen atoms on the His57 imidazole ring and on Ser214 Og were refined with no restraints. s[A]-weighted 2F[o] -F[c] electron density maps are drawn at 2s (cyan). s[A]-weighted F[o] -F[c] maps, calculated prior to the modeling of hydrogen atoms on His57 and hydroxyl groups, are contoured at 3s (green) and 2s (pink).
Figure 5.
Figure 5. Phe228 is distorted by tight packing in the C-terminal domain. Phe228 (orange) is distorted from planarity by nearby Trp199 (red) and Thr181 (yellow). (a) The pro region aLP complex (4PRO.pdb).[48.] aLP is a double b-barrel structure consisting of N-terminal (dark grey) and C-terminal (light grey) domains. The pro region (teal) catalyzes folding of aLP, with most pro region aLP interactions occurring with the C-terminal domain of aLP. Interestingly, the distorted Phe228 is located in the core of the C-terminal domain. For reference, the catalytic triad (Asp102, His57, Ser195) is displayed in green. (b) The distortion of Phe228. The s[A]-weighted 2F[o] -F[c] electron density map is displayed for Phe228 at contour level 2s (cyan). The angle between vectors C^b->C^g and C^g-> C^z is indicated. (c) van der Waals surfaces for a selection of residues within 5 Å of Phe228 show the tight packing in this region.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 338, 999-0) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21396941 S.Cui, J.Wang, T.Fan, B.Qin, L.Guo, X.Lei, J.Wang, M.Wang, and Q.Jin (2011).
Crystal structure of human enterovirus 71 3C protease.
  J Mol Biol, 408, 449-461.
PDB code: 3osy
20195497 N.L.Salimi, B.Ho, and D.A.Agard (2010).
Unfolding simulations reveal the mechanism of extreme unfolding cooperativity in the kinetically stable alpha-lytic protease.
  PLoS Comput Biol, 6, e1000689.  
20421414 T.Pfirrmann, S.Heessen, D.J.Omnus, C.Andréasson, and P.O.Ljungdahl (2010).
The prodomain of Ssy5 protease controls receptor-activated proteolysis of transcription factor Stp1.
  Mol Cell Biol, 30, 3299-3309.  
19240325 J.M.Holton (2009).
A beginner's guide to radiation damage.
  J Synchrotron Radiat, 16, 133-142.  
18808119 P.A.Sigala, D.A.Kraut, J.M.Caaveiro, B.Pybus, E.A.Ruben, D.Ringe, G.A.Petsko, and D.Herschlag (2008).
Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole.
  J Am Chem Soc, 130, 13696-13708.
PDB codes: 2inx 3cpo
19030592 P.K.Wawrzyniak, A.Alia, R.G.Schaap, M.M.Heemskerk, H.J.de Groot, and F.Buda (2008).
Protein-induced geometric constraints and charge transfer in bacteriochlorophyll-histidine complexes in LH2.
  Phys Chem Chem Phys, 10, 6971-6978.  
17211072 J.M.Holton (2007).
XANES measurements of the rate of radiation damage to selenomethionine side chains.
  J Synchrotron Radiat, 14, 51-72.  
17501917 K.Pauwels, I.Van Molle, J.Tommassen, and P.Van Gelder (2007).
Chaperoning Anfinsen: the steric foldases.
  Mol Microbiol, 64, 917-922.  
17131430 V.Helms (2007).
Protein dynamics tightly connected to the dynamics of surrounding and internal water molecules.
  Chemphyschem, 8, 23-33.  
17427287 F.van den Ent, M.Leaver, F.Bendezu, J.Errington, P.de Boer, and J.Löwe (2006).
Dimeric structure of the cell shape protein MreC and its functional implications.
  Mol Microbiol, 62, 1631-1642.
PDB code: 2j5u
16524914 P.Poulsen, L.Lo Leggio, and M.C.Kielland-Brandt (2006).
Mapping of an internal protease cleavage site in the Ssy5p component of the amino acid sensor of Saccharomyces cerevisiae and functional characterization of the resulting pro- and protease domains by gain-of-function genetics.
  Eukaryot Cell, 5, 601-608.  
15983423 H.Bönisch, C.L.Schmidt, P.Bianco, and R.Ladenstein (2005).
Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S.
  Acta Crystallogr D Biol Crystallogr, 61, 990.
PDB codes: 1yk4 1yk5
16044461 S.M.Truhlar, and D.A.Agard (2005).
The folding landscape of an alpha-lytic protease variant reveals the role of a conserved beta-hairpin in the development of kinetic stability.
  Proteins, 61, 105-114.  
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.