PDBsum entry: 1xrp

Hydrolase

PDB id: 1xrp

Contents

Protein chain

290 a.a. *

Ligands

PRO-LEU-GLY-GLY

PRO

Waters ×119

* Residue conservation analysis

PDB id:

1xrp

Name:

Hydrolase

Title:

Crystal structure of active site f1-mutant e213q soaked with peptide pro-leu-gly-gly

Structure:

Proline iminopeptidase. Chain: a. Synonym: pip, prolyl aminopeptidase, pap, tricorn protease interacting factor f1. Engineered: yes. Mutation: yes. Plgg. Chain: q. Engineered: yes

Source:

Thermoplasma acidophilum. Organism_taxid: 2303. Gene: ta0830. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: chemically synthesized

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.220 R-free: 0.296

Authors:

P.Goettig,H.Brandstetter,M.Groll,W.Goehring,P.V.Konarev, D.I.Svergun,R.Huber,J.-S.Kim

Key ref:

P.Goettig et al. (2005). X-ray snapshots of peptide processing in mutants of tricorn-interacting factor F1 from Thermoplasma acidophilum. J Biol Chem, 280, 33387-33396. PubMed id: 15994304 DOI: 10.1074/jbc.M505030200

Date:

15-Oct-04 Release date: 12-Jul-05

Protein chain

P96084  (PIP_THEAC) -  Proline iminopeptidase

Seq: 293 a.a.

Struc: 290 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.4.11.5 - Prolyl aminopeptidase.
• Reaction: Release of a N-terminal proline from a peptide.
• Cofactor: Manganese

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: proteolysis (1 term)
• Biochemical function: hydrolase activity (3 terms)

DOI no: 10.1074/jbc.M505030200

J Biol Chem 280:33387-33396 (2005)

PubMed id: 15994304

X-ray snapshots of peptide processing in mutants of tricorn-interacting factor F1 from Thermoplasma acidophilum.

P.Goettig, H.Brandstetter, M.Groll, W.Göhring, P.V.Konarev, D.I.Svergun, R.Huber, J.S.Kim.

ABSTRACT

The tricorn-interacting factor F1 of the archaeon Thermoplasma acidophilum cleaves small hydrophobic peptide products of the proteasome and tricorn protease. F1 mutants of the active site residues that are involved in substrate recognition and catalysis displayed distinct activity patterns toward fluorogenic test substrates. Crystal structures of the mutant proteins complexed with peptides Phe-Leu, Pro-Pro, or Pro-Leu-Gly-Gly showed interaction of glutamates 213 and 245 with the N termini of the peptides and defined the S1 and S1' sites and the role of the catalytic residues. Evidence was found for processive peptide cleavage in the N-to-C direction, whereby the P1' product is translocated into the S1 site. A functional interaction of F1 with the tricorn protease was observed with the inactive F1 mutant G37A. Moreover, small angle x-ray scattering measurements for tricorn and inhibited F1 have been interpreted as formation of transient and substrate-induced complexes.

Selected figure(s)

Figure 5.
FIGURE 5. Cleavage products of peptides in F1 mutants and inactive G37A in stereo. Electron density is displayed only for relevant residues. A, single proline molecules cleaved from Pro-Pro by mutant E245Q occupy the S1 site and the region of the E1 entrance. The 2F[o] - F[c] electron density map is contoured at 1 . B, leucine, the former P1' residue from the soaked peptide FL, is found in the S1 site of E213Q. The amino acid is depicted in green. The corresponding 2F[o] - F[c] map is contoured at 0.8 . C, the crystal soak with the dipeptide FA in E213Q resulted in a single alanine that is bound in the S1 site mainly by Asn-209 and Gly-37 in contrast to leucine (panel B) or proline (panel A). The 2F[o] - F[c] map is contoured at 1 . D, stereoview of the inactive mutant G37A rotated anticlockwise by 60° around the y axis with respect to the previous images. The carbonyl of Ala-37 forms a hydrogen bond to the O- of Ser-105, and the loop from Gly-36 to Met-40 has moved into the S1' cave blocking access for peptides through the E1 tunnel. Ala-37 and Tyr-106 are displayed in magenta. The 2F[o] - F[c] map (contour level 1 ) covers Tyr-106, which partially occupies the S1 site, and the loop from Gly-36 to Met-40. The backbone of WT-F1 is superimposed as white sticks.

Figure 6.
FIGURE 6. Model of the complex between F1 and tricorn bound with their most complementary surfaces. Both peptidases are depicted with molecular surfaces and ribbon plots. The catalytic serines 105 (F1) and 965, glutamates 213 and 245 of F1 and the arginine gate (Arg-131 and 132) of tricorn are shown as black sticks, indicated as Ser, Args, and Glus. In this orientation the peptide PLGG (black stick model) that was bound to E213Q near the E1 entrance of F1 is located with its C terminus at the mouth of the outlet tunnel of the 6-propeller domain, which is indicated as well as the 7-propeller domain of tricorn.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 33387-33396) copyright 2005.

Figures were selected by an automated process.