PDB ID or protein name

1kn9 » Type 1 signal peptidase, apo-enzyme

1kn9 » Type 1 signal peptidase, apo-enzyme
Magnify 1kn9 » Type 1 signal peptidase, apo-enzymeEnlarged view of image
3D view in Jmol or Webmol

gray dot

Download Coordinates

gray dot

Topology in Bacterial Gram-negative inner membrane
Topologyout side
in side
1kn9 » Type 1 signal peptidase, apo-enzyme
Hydrophobic Thickness 3.4 ± 1.4 Å
Tilt Angle 80 ± 6°
ΔGtransfer -7.8 kcal/mol
Links to 1kn9 PDB Sum, PDB, SCOP, MSD, OCA, MMDB
Topology out
Resolution 2.4 Å
Other PDB entries representing this structure none
Number of TM subunits 1
Experimental Verification for 1kn9 » Type 1 signal peptidase, apo-enzyme
This is a two-pass TM protein (Uniprot). The isolated periplasmic domain des(2-75) is catalytically active (Paetzel et al. 2002) and associates with lipid bilayers (van Klompenburg et al. 1998, van den Brink-van der Laan et al. 2001). It inserts preferentially into bilayers with decreased headgroup lateral pressure (van den Brink-van der Laan et al. 2004). The following residues of the apo-enzyme are buried in the membrane interior: W300, M301, F303, L314, and L316. This is consistent with the important role of W300 for membrane association (Kim et al. 1995) and with location of N-terminal membrane-anchoring domain. Calculated orientation is similar to that proposed by Paetzel et al. (1998).
6 references
Kim YT, Muramatsu T, Takahashi K. 1995. Identification of Trp300 as an important residue for Escherichia coli leader peptidase activity. Eur J Biochem. 234:358-62. PubMed
Paetzel M, Dalbey RE, Strynadka NC. 1998. Crystal structure of a bacterial signal peptidase in complex with a beta-lactam inhibitor. Nature. 396:186-90. PubMed
Paetzel M, Karla A, Strynadka NC, Dalbey RE. 2002. Signal peptidases. Chem Rev. 102: 4549-80. PubMed
van den Brink-van der Laan E, Dalbey RE, Demel RA, Killian JA, de Kruijff B. 2001. Effect of nonbilayer lipids on membrane binding and insertion of the catalytic domain of leader peptidase. Biochemistry. 40: 9677-9684. PubMed
van den Brink-van der Laan E, Killian JA, de Kruijff B. 2004. Nonbilayer lipids affect peripheral and integral membrane proteins via changes in the lateral pressure profile. Biochim Biophys Acta. 1666: 275-88. PubMed
van Klompenburg W, Paetzel M, de Jong JM, Dalbey RE, Demel RA, von Heijne G, de Kruijff B. 1998. Phosphatidylethanolamine mediates insertion of the catalytic domain of leader peptidase in membranes. FEBS Lett. 431: 75-79. PubMed
Comments on 1kn9 » Type 1 signal peptidase, apo-enzyme
Function - see review by Paetzel et al. (2002).