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PDBsum entry 2dkf
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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 ttha0252 from thermus thermophilus hb8, a RNA degradation protein of the metallo-beta-lactamase superfamily
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Structure:
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Metallo-beta-lactamase superfamily protein. Chain: a, b, c, d. Synonym: ttha0252 protein. Engineered: yes
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Source:
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Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Gene: ttha0252. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Biol. unit:
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Monomer (from
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Resolution:
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2.80Å
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R-factor:
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0.242
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R-free:
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0.285
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Authors:
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I.Ishikawa,N.Nakagawa,S.Kuramitsu,S.Yokoyama,R.Masui,Riken Structural Genomics/proteomics Initiative (Rsgi)
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Key ref:
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H.Ishikawa
et al.
(2006).
Crystal structure of TTHA0252 from Thermus thermophilus HB8, a RNA degradation protein of the metallo-beta-lactamase superfamily.
J Biochem (tokyo),
140,
535-542.
PubMed id:
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Date:
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10-Apr-06
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Release date:
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05-Dec-06
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PROCHECK
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Headers
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References
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Q5SLP1
(RNSE_THET8) -
Ribonuclease TTHA0252 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
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Seq:
Struc:
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431 a.a.
431 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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J Biochem (tokyo)
140:535-542
(2006)
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PubMed id:
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Crystal structure of TTHA0252 from Thermus thermophilus HB8, a RNA degradation protein of the metallo-beta-lactamase superfamily.
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H.Ishikawa,
N.Nakagawa,
S.Kuramitsu,
R.Masui.
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ABSTRACT
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In bacterial RNA metabolism, mRNA degradation is an important process for gene
expression. Recently, a novel ribonuclease (RNase), belonging to the beta-CASP
family within the metallo-beta-lactamase superfamily, was identified as a
functional homologue of RNase E, a major component for mRNA degradation in
Escherichia coli. Here, we have determined the crystal structure of TTHA0252
from Thermus thermophilus HB8, which represents the first report of the tertiary
structure of a beta-CASP family protein. TTHA0252 comprises two separate
domains: a metallo-beta-lactamase domain and a "clamp" domain. The active site
of the enzyme is located in a cleft between the two domains, which includes two
zinc ions coordinated by seven conserved residues. Although this configuration
is similar to those of other beta-lactamases, TTHA0252 has one conserved His
residue characteristic of the beta-CASP family as a ligand. We also detected
nuclease activity of TTHA0252 against rRNAs of T. thermophilus. Our results
reveal structural and functional aspects of novel RNase E-like enzymes with a
beta-CASP fold.
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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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A.Shimada,
H.Ishikawa,
N.Nakagawa,
S.Kuramitsu,
and
R.Masui
(2010).
The first crystal structure of an archaeal metallo-beta-lactamase superfamily protein; ST1585 from Sulfolobus tokodaii.
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Proteins,
78,
2399-2402.
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PDB code:
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F.Alaleona,
S.Franceschini,
P.Ceci,
A.Ilari,
and
E.Chiancone
(2010).
Thermosynechococcus elongatus DpsA binds Zn(II) at a unique three histidine-containing ferroxidase center and utilizes O2 as iron oxidant with very high efficiency, unlike the typical Dps proteins.
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FEBS J,
277,
903-917.
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PDB code:
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Y.Nishida,
H.Ishikawa,
S.Baba,
N.Nakagawa,
S.Kuramitsu,
and
R.Masui
(2010).
Crystal structure of an archaeal cleavage and polyadenylation specificity factor subunit from Pyrococcus horikoshii.
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Proteins,
78,
2395-2398.
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PDB codes:
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C.R.Mandel,
Y.Bai,
and
L.Tong
(2008).
Protein factors in pre-mRNA 3'-end processing.
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Cell Mol Life Sci,
65,
1099-1122.
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I.L.de la Sierra-Gallay,
L.Zig,
A.Jamalli,
and
H.Putzer
(2008).
Structural insights into the dual activity of RNase J.
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Nat Struct Mol Biol,
15,
206-212.
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PDB codes:
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N.G.Kolev,
T.A.Yario,
E.Benson,
and
J.A.Steitz
(2008).
Conserved motifs in both CPSF73 and CPSF100 are required to assemble the active endonuclease for histone mRNA 3'-end maturation.
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EMBO Rep,
9,
1013-1018.
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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
code is
shown on the right.
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Links
