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* Residue conservation analysis
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PDB id:
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Hydrolase
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Title:
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Crystal structure of sulfolobus solfataricus peptidyl-tRNA hydrolase
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Structure:
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Peptidyl-tRNA hydrolase. Chain: a, b, c, d. Synonym: pth. Engineered: yes
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Source:
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Pyrococcus abyssi. Organism_taxid: 29292. Strain: dsm1617. Gene: pth. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Dimer (from
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Resolution:
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1.80Å
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R-factor:
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0.205
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R-free:
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0.224
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Authors:
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M.Fromant,E.Schmitt,Y.Mechulam,C.Lazennec,P.Plateau, S.Blanquet
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Key ref:
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M.Fromant
et al.
(2005).
Crystal structure at 1.8 A resolution and identification of active site residues of Sulfolobus solfataricus peptidyl-tRNA hydrolase.
Biochemistry,
44,
4294-4301.
PubMed id:
DOI:
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Date:
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25-Oct-04
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Release date:
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22-Mar-05
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PROCHECK
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Headers
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References
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Q980V1
(PTH_SULSO) -
Peptidyl-tRNA hydrolase
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Seq:
Struc:
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120 a.a.
120 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.3.1.1.29
- Aminoacyl-tRNA hydrolase.
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Reaction:
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N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA
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N-substituted aminoacyl-tRNA
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+
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H(2)O
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=
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N-substituted amino acid
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+
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tRNA
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Cellular component
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cytoplasm
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1 term
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Biological process
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translation
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1 term
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Biochemical function
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hydrolase activity
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2 terms
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DOI no:
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Biochemistry
44:4294-4301
(2005)
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PubMed id:
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Crystal structure at 1.8 A resolution and identification of active site residues of Sulfolobus solfataricus peptidyl-tRNA hydrolase.
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M.Fromant,
E.Schmitt,
Y.Mechulam,
C.Lazennec,
P.Plateau,
S.Blanquet.
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ABSTRACT
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The 3-D structure of the peptidyl-tRNA hydrolase from the archaea Sulfolobus
solfataricus has been solved at 1.8 A resolution. Homologues of this enzyme are
found in archaea and eucarya. Bacteria display a different type of peptidyl-tRNA
hydrolase that is also encountered in eucarya. In solution, the S. solfataricus
hydrolase behaves as a dimer. In agreement, the crystalline structure of this
enzyme indicates the formation of a dimer. Each protomer is made of a mixed
five-stranded beta-sheet surrounded by two groups of two alpha-helices. The
dimer interface is mainly formed by van der Waals interactions between
hydrophobic residues belonging to the two N-terminal alpha1 helices contributed
by two protomers. Site-directed mutagenesis experiments were designed for
probing the basis of specificity of the archaeal hydrolase. Among the strictly
conserved residues within the archaeal/eucaryal peptidyl-tRNA hydrolase family,
three residues, K18, D86, and T90, appear of utmost importance for activity.
They are located in the N-part of alpha1 and in the beta3-beta4 loop. K18 and
D86, which form a salt bridge, might play a role in the catalysis thanks to
their acid and basic functions, whereas the OH group of T90 could act as a
nucleophile. These observations clearly distinguish the active site of the
archaeal/eucaryal hydrolases from that of the bacterial/eucaryal ones, where a
histidine is believed to serve as the catalytic base.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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K.Shimizu,
C.Kuroishi,
M.Sugahara,
and
N.Kunishima
(2008).
Structure of peptidyl-tRNA hydrolase 2 from Pyrococcus horikoshii OT3: insight into the functional role of its dimeric state.
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Acta Crystallogr D Biol Crystallogr, 64,
444-453.
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PDB codes:
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N.C.Bal,
H.Agrawal,
A.K.Meher,
and
A.Arora
(2007).
Characterization of peptidyl-tRNA hydrolase encoded by open reading frame Rv1014c of Mycobacterium tuberculosis H37Rv.
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Biol Chem, 388,
467-479.
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M.L.Ferri-Fioni,
M.Fromant,
A.P.Bouin,
C.Aubard,
C.Lazennec,
P.Plateau,
and
S.Blanquet
(2006).
Identification in archaea of a novel D-Tyr-tRNATyr deacylase.
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J Biol Chem, 281,
27575-27585.
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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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Links
