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PDBsum entry 1b12
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Hydrolase PDB id
1b12

 

 

 

 

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Contents
Protein chains
239 a.a. *
211 a.a. *
226 a.a. *
222 a.a. *
Ligands
1PN ×4
PO4
Waters ×448
* Residue conservation analysis
PDB id:
1b12
Name: Hydrolase
Title: Crystal structure of type 1 signal peptidase from escherichia coli in complex with a beta-lactam inhibitor
Structure: Signal peptidase i. Chain: a, b, c, d. Fragment: catalytic domain. Synonym: spase i, leader peptidase i. Engineered: yes
Source: Escherichia coli. Organism_taxid: 469008. Strain: bl21(de3). Cellular_location: periplasm. Gene: lepb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.95Å     R-factor:   0.220     R-free:   0.246
Authors: M.Paetzel,R.Dalbey,N.C.J.Strynadka
Key ref:
M.Paetzel et al. (1998). Crystal structure of a bacterial signal peptidase in complex with a beta-lactam inhibitor. Nature, 396, 186-190. PubMed id: 9823901 DOI: 10.1038/24196
Date:
24-Nov-99     Release date:   10-Dec-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P00803  (LEP_ECOLI) -  Signal peptidase I from Escherichia coli (strain K12)
Seq:
Struc: 		324 a.a.
239 a.a.
Protein chain
P00803  (LEP_ECOLI) -  Signal peptidase I from Escherichia coli (strain K12)
Seq:
Struc: 		324 a.a.
211 a.a.
Protein chain
P00803  (LEP_ECOLI) -  Signal peptidase I from Escherichia coli (strain K12)
Seq:
Struc: 		324 a.a.
226 a.a.
Protein chain
P00803  (LEP_ECOLI) -  Signal peptidase I from Escherichia coli (strain K12)
Seq:
Struc: 		324 a.a.
222 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.3.4.21.89  - signal peptidase I.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Cleavage of N-terminal leader sequences from secreted and periplasmic proteins precursor.

 

 
DOI no: 10.1038/24196 Nature 396:186-190 (1998)
PubMed id: 9823901  
 
 
Crystal structure of a bacterial signal peptidase in complex with a beta-lactam inhibitor.
M.Paetzel, R.E.Dalbey, N.C.Strynadka.
 
  ABSTRACT  
 
The signal peptidase (SPase) from Escherichia coli is a membrane-bound endopeptidase with two amino-terminal transmembrane segments and a carboxy-terminal catalytic region which resides in the periplasmic space. SPase functions to release proteins that have been translocated into the inner membrane from the cell interior, by cleaving off their signal peptides. We report here the X-ray crystal structure of a catalytically active soluble fragment of E. coli SPase (SPase delta2-75). We have determined this structure at 1.9 A resolution in a complex with an inhibitor, a beta-lactam (5S,6S penem), which is covalently bound as an acyl-enzyme intermediate to the gamma-oxygen of a serine residue at position 90, demonstrating that this residue acts as the nucleophile in the hydrolytic mechanism of signal-peptide cleavage. The structure is consistent with the use by SPase of Lys 145 as a general base in the activation of the nucleophilic Ser90, explains the specificity requirement at the signal-peptide cleavage site, and reveals a large exposed hydrophobic surface which could be a site for an intimate association with the membrane. As enzymes that are essential for cell viability, bacterial SPases present a feasible antibacterial target: our determination of the SPase structure therefore provides a template for the rational design of antibiotic compounds.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 Structure of the -lactam-type inhibitor allyl (5S,6S)-6-[(R)-acetoxyethyl]penem-3-carboxylateup.4,5. 		Figure 5.
Figure 5 A ball-and-stick representation30 of the active-site residues of SPase 2-75 with the P1-P4 residues of an acylated peptide substrate (Ala-Ala-Ala-Ala) modelled into the bindings sites S1-S4. The observed positions of the methyl group (C16) and the carbonyl oxygen (O8) of the inhibitor (Fig. 4) were used as a guide.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1998, 396, 186-190) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22683878 T.Palmer, and B.C.Berks (2012).
The twin-arginine translocation (Tat) protein export pathway.
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20070259 S.Urban (2010).
Taking the plunge: integrating structural, enzymatic and computational insights into a unified model for membrane-immersed rhomboid proteolysis.
  Biochem J, 425, 501-512.  
19696105 K.Bockstael, N.Geukens, L.Van Mellaert, P.Herdewijn, J.Anné, and A.Van Aerschot (2009).
Evaluation of the type I signal peptidase as antibacterial target for biofilm-associated infections of Staphylococcus epidermidis.
  Microbiology, 155, 3719-3729.  
19246745 K.Watanabe, Y.Tsuchida, N.Okibe, H.Teramoto, N.Suzuki, M.Inui, and H.Yukawa (2009).
Scanning the Corynebacterium glutamicum R genome for high-efficiency secretion signal sequences.
  Microbiology, 155, 741-750.  
18840693 C.Lundin, H.Kim, I.Nilsson, S.H.White, and G.von Heijne (2008).
Molecular code for protein insertion in the endoplasmic reticulum membrane is similar for N(in)-C(out) and N(out)-C(in) transmembrane helices.
  Proc Natl Acad Sci U S A, 105, 15702-15707.  
18315846 K.H.Choo, J.C.Tong, and S.Ranganathan (2008).
Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage.
  BMC Bioinformatics, 9, S15.  
18177734 M.Musial-Siwek, D.A.Kendall, and P.L.Yeagle (2008).
Solution NMR of signal peptidase, a membrane protein.
  Biochim Biophys Acta, 1778, 937-944.  
18476724 P.Wang, E.Shim, B.Cravatt, R.Jacobsen, J.Schoeniger, A.C.Kim, M.Paetzel, and R.E.Dalbey (2008).
Escherichia coli signal peptide peptidase A is a serine-lysine protease with a lysine recruited to the nonconserved amino-terminal domain in the S49 protease family.
  Biochemistry, 47, 6361-6369.  
17603894 A.L.Lomize, I.D.Pogozheva, M.A.Lomize, and H.I.Mosberg (2007).
The role of hydrophobic interactions in positioning of peripheral proteins in membranes.
  BMC Struct Biol, 7, 44.  
17239231 G.Jékely (2007).
Origin of phagotrophic eukaryotes as social cheaters in microbial biofilms.
  Biol Direct, 2, 3.  
17672887 G.Mayr, F.S.Domingues, and P.Lackner (2007).
Comparative analysis of protein structure alignments.
  BMC Struct Biol, 7, 50.  
17185295 J.H.Ahn, M.Y.Hwang, K.H.Lee, C.Y.Choi, and D.M.Kim (2007).
Use of signal sequences as an in situ removable sequence element to stimulate protein synthesis in cell-free extracts.
  Nucleic Acids Res, 35, e21.  
17553791 J.Lee, A.R.Feldman, B.Delmas, and M.Paetzel (2007).
Crystal structure of the VP4 protease from infectious pancreatic necrosis virus reveals the acyl-enzyme complex for an intermolecular self-cleavage reaction.
  J Biol Chem, 282, 24928-24937.
PDB codes: 2pnl 2pnm
17077081 O.D.Ekici, A.Karla, M.Paetzel, M.O.Lively, D.Pei, and R.E.Dalbey (2007).
Altered -3 substrate specificity of Escherichia coli signal peptidase 1 mutants as revealed by screening a combinatorial peptide library.
  J Biol Chem, 282, 417-425.  
17676771 S.L.Rusch, and D.A.Kendall (2007).
Interactions that drive Sec-dependent bacterial protein transport.
  Biochemistry, 46, 9665-9673.  
17277078 Y.Wang, and Y.Ha (2007).
Open-cap conformation of intramembrane protease GlpG.
  Proc Natl Acad Sci U S A, 104, 2098-2102.
PDB code: 2o7l
16484202 A.Fine, V.Irihimovitch, I.Dahan, Z.Konrad, and J.Eichler (2006).
Cloning, expression, and purification of functional Sec11a and Sec11b, type I signal peptidases of the archaeon Haloferax volcanii.
  J Bacteriol, 188, 1911-1919.  
  16582483 J.Lee, A.R.Feldman, B.Delmas, and M.Paetzel (2006).
Expression, purification and crystallization of a birnavirus-encoded protease, VP4, from blotched snakehead virus (BSNV).
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 353-356.  
  17142905 J.Lee, A.R.Feldman, E.Chiu, C.Chan, Y.N.Kim, B.Delmas, and M.Paetzel (2006).
Purification, crystallization and preliminary X-ray analysis of truncated and mutant forms of VP4 protease from infectious pancreatic necrosis virus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1235-1238.  
16484219 R.Matsumi, H.Atomi, and T.Imanaka (2006).
Identification of the amino acid residues essential for proteolytic activity in an archaeal signal peptide peptidase.
  J Biol Chem, 281, 10533-10539.  
17051161 Y.Wang, Y.Zhang, and Y.Ha (2006).
Crystal structure of a rhomboid family intramembrane protease.
  Nature, 444, 179-180.
PDB code: 2ic8
16148304 J.Eichler, and M.W.Adams (2005).
Posttranslational protein modification in Archaea.
  Microbiol Mol Biol Rev, 69, 393-425.  
15814844 L.Burri, Y.Strahm, C.J.Hawkins, I.E.Gentle, M.A.Puryer, A.Verhagen, B.Callus, D.Vaux, and T.Lithgow (2005).
Mature DIABLO/Smac is produced by the IMP protease complex on the mitochondrial inner membrane.
  Mol Biol Cell, 16, 2926-2933.  
15765498 N.Jessani, J.A.Young, S.L.Diaz, M.P.Patricelli, A.Varki, and B.F.Cravatt (2005).
Class assignment of sequence-unrelated members of enzyme superfamilies by activity-based protein profiling.
  Angew Chem Int Ed Engl, 44, 2400-2403.  
15187182 H.Tjalsma, H.Antelmann, J.D.Jongbloed, P.G.Braun, E.Darmon, R.Dorenbos, J.Y.Dubois, H.Westers, G.Zanen, W.J.Quax, O.P.Kuipers, S.Bron, M.Hecker, and J.M.van Dijl (2004).
Proteomics of protein secretion by Bacillus subtilis: separating the "secrets" of the secretome.
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14665623 I.Botos, E.E.Melnikov, S.Cherry, J.E.Tropea, A.G.Khalatova, F.Rasulova, Z.Dauter, M.R.Maurizi, T.V.Rotanova, A.Wlodawer, and A.Gustchina (2004).
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15579213 M.Hopfe, R.Hoffmann, and B.Henrich (2004).
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15132751 M.Miot, and J.M.Betton (2004).
Protein quality control in the bacterial periplasm.
  Microb Cell Fact, 3, 4.  
15136583 M.Paetzel, J.J.Goodall, M.Kania, R.E.Dalbey, and M.G.Page (2004).
Crystallographic and biophysical analysis of a bacterial signal peptidase in complex with a lipopeptide-based inhibitor.
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15456757 Y.J.Im, Y.Na, G.B.Kang, S.H.Rho, M.K.Kim, J.H.Lee, C.H.Chung, and S.H.Eom (2004).
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  J Biol Chem, 279, 53451-53457.
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Crystal structures of Staphylococcus aureus sortase A and its substrate complex.
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PDB codes: 1t2o 1t2p 1t2w
12771148 D.T.Rutkowski, C.M.Ott, J.R.Polansky, and V.R.Lingappa (2003).
Signal sequences initiate the pathway of maturation in the endoplasmic reticulum lumen.
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12813070 E.van den Brink-van der Laan, J.W.Boots, R.E.Spelbrink, G.M.Kool, E.Breukink, J.A.Killian, and B.de Kruijff (2003).
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14559916 H.Liang, C.VanValkenburgh, X.Chen, C.Mullins, L.Van Kaer, N.Green, and H.Fang (2003).
Genetic complementation in yeast reveals functional similarities between the catalytic subunits of mammalian signal peptidase complex.
  J Biol Chem, 278, 50932-50939.  
12761228 I.Nilsson, A.E.Johnson, and G.von Heijne (2003).
How hydrophobic is alanine?
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Molecular analysis of Phr peptide processing in Bacillus subtilis.
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14526003 S.Y.Ng, and K.F.Jarrell (2003).
Cloning and characterization of archaeal type I signal peptidase from Methanococcus voltae.
  J Bacteriol, 185, 5936-5942.  
12482857 W.Luo, X.Chen, H.Fang, and N.Green (2003).
Factors governing nonoverlapping substrate specificity by mitochondrial inner membrane peptidase.
  J Biol Chem, 278, 4943-4948.  
12393890 A.V.Kajava, S.N.Zolov, K.I.Pyatkov, A.E.Kalinin, and M.A.Nesmeyanova (2002).
Processing of Escherichia coli alkaline phosphatase. Sequence requirements and possible conformations of the -6 to -4 region of the signal peptide.
  J Biol Chem, 277, 50396-50402.  
12384363 M.D.Barbosa, S.Lin, J.A.Markwalder, J.A.Mills, J.A.DeVito, C.A.Teleha, V.Garlapati, C.Liu, A.Thompson, G.L.Trainor, M.G.Kurilla, and D.L.Pompliano (2002).
Regulated expression of the Escherichia coli lepB gene as a tool for cellular testing of antimicrobial compounds that inhibit signal peptidase I in vitro.
  Antimicrob Agents Chemother, 46, 3549-3554.  
11835278 M.Gonzalez, and R.Woodgate (2002).
The "tale" of UmuD and its role in SOS mutagenesis.
  Bioessays, 24, 141-148.  
11741964 M.Paetzel, R.E.Dalbey, and N.C.Strynadka (2002).
Crystal structure of a bacterial signal peptidase apoenzyme: implications for signal peptide binding and the Ser-Lys dyad mechanism.
  J Biol Chem, 277, 9512-9519.
PDB code: 1kn9
11741926 N.A.Sharkov, and D.Cai (2002).
Discovery of substrate for type I signal peptidase SpsB from Staphylococcus aureus.
  J Biol Chem, 277, 5796-5803.  
12032064 S.Shin, T.H.Lee, N.C.Ha, H.M.Koo, S.Y.Kim, H.S.Lee, Y.S.Kim, and B.H.Oh (2002).
Structure of malonamidase E2 reveals a novel Ser-cisSer-Lys catalytic triad in a new serine hydrolase fold that is prevalent in nature.
  EMBO J, 21, 2509-2516.
PDB codes: 1ock 1ocl 1ocm
11806909 T.J.Minehardt, N.Marzari, R.Cooke, E.Pate, P.A.Kollman, and R.Car (2002).
A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP.
  Biophys J, 82, 660-675.  
11483531 A.E.Ferentz, G.C.Walker, and G.Wagner (2001).
Converting a DNA damage checkpoint effector (UmuD2C) into a lesion bypass polymerase (UmuD'2C).
  EMBO J, 20, 4287-4298.
PDB code: 1i4v
11285222 A.Rehm, P.Stern, H.L.Ploegh, and D.Tortorella (2001).
Signal peptide cleavage of a type I membrane protein, HCMV US11, is dependent on its membrane anchor.
  EMBO J, 20, 1573-1582.  
11114935 M.D.Sutton, M.Kim, and G.C.Walker (2001).
Genetic and biochemical characterization of a novel umuD mutation: insights into a mechanism for UmuD self-cleavage.
  J Bacteriol, 183, 347-357.  
11133956 S.B.Peng, L.Wang, J.Moomaw, R.B.Peery, P.M.Sun, R.B.Johnson, J.Lu, P.Treadway, P.L.Skatrud, and Q.M.Wang (2001).
Biochemical characterization of signal peptidase I from gram-positive Streptococcus pneumoniae.
  J Bacteriol, 183, 621-627.  
11350936 T.L.Yahr, and W.T.Wickner (2001).
Functional reconstitution of bacterial Tat translocation in vitro.
  EMBO J, 20, 2472-2479.  
10828968 A.N.Ridder, S.Morein, J.G.Stam, A.Kuhn, B.de Kruijff, and J.A.Killian (2000).
Analysis of the role of interfacial tryptophan residues in controlling the topology of membrane proteins.
  Biochemistry, 39, 6521-6528.  
10619850 C.Birghan, E.Mundt, and A.E.Gorbalenya (2000).
A non-canonical lon proteinase lacking the ATPase domain employs the ser-Lys catalytic dyad to exercise broad control over the life cycle of a double-stranded RNA virus.
  EMBO J, 19, 114-123.  
10590087 E.Lee, C.E.Stocks, S.M.Amberg, C.M.Rice, and M.Lobigs (2000).
Mutagenesis of the signal sequence of yellow fever virus prM protein: enhancement of signalase cleavage In vitro is lethal for virus production.
  J Virol, 74, 24-32.  
10974125 H.Tjalsma, A.Bolhuis, J.D.Jongbloed, S.Bron, and J.M.van Dijl (2000).
Signal peptide-dependent protein transport in Bacillus subtilis: a genome-based survey of the secretome.
  Microbiol Mol Biol Rev, 64, 515-547.  
10852727 J.L.Carlos, P.A.Klenotic, M.Paetzel, N.C.Strynadka, and R.E.Dalbey (2000).
Mutational evidence of transition state stabilization by serine 88 in Escherichia coli type I signal peptidase.
  Biochemistry, 39, 7276-7283.  
10805775 J.Ye, U.P.Davé, N.V.Grishin, J.L.Goldstein, and M.S.Brown (2000).
Asparagine-proline sequence within membrane-spanning segment of SREBP triggers intramembrane cleavage by site-2 protease.
  Proc Natl Acad Sci U S A, 97, 5123-5128.  
11004175 M.L.van Roosmalen, J.D.Jongbloed, A.Kuipers, G.Venema, S.Bron, and J.M.van DijL (2000).
A truncated soluble Bacillus signal peptidase produced in Escherichia coli is subject to self-cleavage at its active site.
  J Bacteriol, 182, 5765-5770.  
10692453 P.A.Klenotic, J.L.Carlos, J.C.Samuelson, T.A.Schuenemann, W.R.Tschantz, M.Paetzel, N.C.Strynadka, and R.E.Dalbey (2000).
The role of the conserved box E residues in the active site of the Escherichia coli type I signal peptidase.
  J Biol Chem, 275, 6490-6498.  
11073921 R.Eisenbrandt, M.Kalkum, R.Lurz, and E.Lanka (2000).
Maturation of IncP pilin precursors resembles the catalytic Dyad-like mechanism of leader peptidases.
  J Bacteriol, 182, 6751-6761.  
10666235 S.Petit, N.Lejal, J.C.Huet, and B.Delmas (2000).
Active residues and viral substrate cleavage sites of the protease of the birnavirus infectious pancreatic necrosis virus.
  J Virol, 74, 2057-2066.  
10336490 A.Bolhuis, H.Tjalsma, K.Stephenson, C.R.Harwood, G.Venema, S.Bron, and J.M.van Dijl (1999).
Different mechanisms for thermal inactivation of Bacillus subtilis signal peptidase mutants.
  J Biol Chem, 274, 15865-15868.  
10206957 C.VanValkenburgh, X.Chen, C.Mullins, H.Fang, and N.Green (1999).
The catalytic mechanism of endoplasmic reticulum signal peptidase appears to be distinct from most eubacterial signal peptidases.
  J Biol Chem, 274, 11519-11525.  
10497172 H.Tjalsma, G.Zanen, G.Venema, S.Bron, and J.M.van Dijl (1999).
The potential active site of the lipoprotein-specific (type II) signal peptidase of Bacillus subtilis.
  J Biol Chem, 274, 28191-28197.  
  10559166 M.P.McLenigan, O.I.Kulaeva, D.G.Ennis, A.S.Levine, and R.Woodgate (1999).
The bacteriophage P1 HumD protein is a functional homolog of the prokaryotic UmuD'-like proteins and facilitates SOS mutagenesis in Escherichia coli.
  J Bacteriol, 181, 7005-7013.  
  10595561 M.Paetzel, and N.C.Strynadka (1999).
Common protein architecture and binding sites in proteases utilizing a Ser/Lys dyad mechanism.
  Protein Sci, 8, 2533-2536.  
10455164 P.Taylor, V.Anderson, J.Dowden, S.L.Flitsch, N.J.Turner, K.Loughran, and M.D.Walkinshaw (1999).
Novel mechanism of inhibition of elastase by beta-lactams is defined by two inhibitor crystal complexes.
  J Biol Chem, 274, 24901-24905.  
10608835 X.Chen, C.Van Valkenburgh, H.Fang, and N.Green (1999).
Signal peptides having standard and nonstandard cleavage sites can be processed by Imp1p of the mitochondrial inner membrane protease.
  J Biol Chem, 274, 37750-37754.  
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 codes are shown on the right.

 

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