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PDBsum entry 3eoq
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References listed in PDB file
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Key reference
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Title
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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.
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Authors
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J.Ohtsuka,
Y.Ichihara,
A.Ebihara,
K.Nagata,
M.Tanokura.
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Ref.
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Proteins, 2009,
75,
774-780.
[DOI no: ]
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PubMed id
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Abstract
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No abstract given.
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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  HxxEHx  are
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.
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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.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2009,
75,
774-780)
copyright 2009.
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