PDBsum entry 3eoq

Hydrolase

PDB id: 3eoq

Contents

Protein chains

405 a.a. *

Waters ×304

* Residue conservation analysis

PDB id:

3eoq

Name:

Hydrolase

Title:

The crystal structure of putative zinc protease beta-subunit from thermus thermophilus hb8

Structure:

Putative zinc protease. Chain: a, b. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Strain: hb8. Gene: ttha1264. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.29Å R-factor: 0.190 R-free: 0.237

Authors:

J.Ohtsuka,Y.Ichihara,A.Ebihara,S.Yokoyama,S.Kuramitsu,K.Nagata, M.Tanokura

Key ref:

J.Ohtsuka et al. (2009). Crystal structure of TTHA1264, a putative M16-family zinc peptidase from Thermus thermophilus HB8 that is homologous to the beta subunit of mitochondrial processing peptidase. Proteins, 75, 774-780. PubMed id: 19241474 DOI: 10.1002/prot.22365

Date:

29-Sep-08 Release date: 17-Mar-09

Protein chains

Q5SIV0  (Q5SIV0_THET8) -  Zinc protease from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 406 a.a.

Struc: 405 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.24.56 - insulysin.
• Reaction: Degradation of insulin, glucagon and other polypeptides. No action on proteins.
• Cofactor: Zn(2+)

DOI no: 10.1002/prot.22365

Proteins 75:774-780 (2009)

PubMed id: 19241474

Crystal structure of TTHA1264, a putative M16-family zinc peptidase from Thermus thermophilus HB8 that is homologous to the beta subunit of mitochondrial processing peptidase.

J.Ohtsuka, Y.Ichihara, A.Ebihara, K.Nagata, M.Tanokura.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. Amino acid sequence properties of M16B peptidase family members. A: Domain structures of the M16 peptidase family. The residues of the zinc-binding motif HxxEHxare represented as vertical dotted lines. The glycine-rich region of MPP is indicated by a black filled box. The abbreviations of the representative proteins are on the left side. IDE, insulin-degrading enzyme; Ptr, pitrilysin; MPP, -subunit of mitochondrial processing peptidase; Core1, core domain 1 of cytochrome bc1 complex; RPP, rickettsial processing peptidase; ppBH4, putative peptidase of Bacillus halodurans H4; [74][alpha.gif] MPP, -subunit of mitochondrial processing peptidase; Core 2, core domain 2 of cytochrome bc1 complex; PreP, presequence peptidase; EuPtr, eupitrilysin. B: Multiple sequence alignment of prokaryotic MPP homologues retrieved at SSDB (http://www.genome.jp/kegg/ssdb/). The UniProt accession numbers are Q5SIV0 (Thermus thermophilus HB8), Q1IW66 (Deinococcus geothermalis), Q7ULM7 (Rhodopirellula baltica), Q5P733 (Azoarcus sp. EbN1), Q479N3 (Dechloromonas aromatica), A1WZF7 (Halorhodospira halophila), Q2JSQ8 (Cyanobacteria Yellowstone A-Prime), Q7NHF1 (Gloeobacter violaceus), and Q7U7A2 (Synechococcus sp. WH8102). The secondary structure elements of TTHA1264 are shown above each column.

Figure 2.
Figure 2. The structure of TTHA1264 and its related structures. A: The stereo view of the overall cartoon representation and secondary structure assignment of the monomer of TTHA1264. The secondary structures determined by modified DSSP[28] at ESPript[21] are colored in red ( -helices), yellow ( -strand), orange (3[10]-helices), and green (random coil). B: The topological diagram of the main-chain trace of TTHA1264. The - and 3[10]-helices are represented as filled red circles and smaller filled orange circles, respectively. The -strands are represented as yellow triangles with the relative backbone directions. Residue numbers at both ends of the secondary structure elements are indicated. C: The zinc-binding motif and the surrounding residues of TTHA1264 (gray) and MPP (orange). The coordinates of the C atoms in 1 of TTHA1264 were superposed on the corresponding atoms of MPP by PyMOL.[27] The residues in zinc-binding motifs are represented as stick models. The zinc ion (gray) and the catalytic water molecule (orange) of MPP are shown as spheres. A water molecule of TTHA1264 corresponding to the catalytic water is represented as a gray sphere. Additional glutamate residues (Glu118 of TTHA1264 and Glu143 of MPP) are also shown as stick models. D: Oligomerization state analysis of TTHA1264 by gel filtration chromatography. Peaks of three standard proteins are shown in green (aldolase, MW = 158,000), cyan (conalbumin, MW = 75,000), and red (ribonuclease A, MW = 13,700). The elution volumes and the logarithmic molecular weights of the three proteins are plotted on the chromatogram (open circles). Molecular weight of TTHA1264 (purple) was estimated (open triangle) to be 47,000 by the regression lines of the three standard data points. E: The representations of electrostatic potentials on the solvent accessible surface of the heterodimeric MPP, homodimeric TTHA1264, and heterodimeric Core. The black dotted open circles indicate the location of the zinc-binding motifs, represented as stick model. The black dotted open square indicates the glycine-rich loop in MPP. The potentials displayed represent a range from -20 (red) to +20 (blue) k[B]T.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2009, 75, 774-780) copyright 2009.