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PDBsum entry 4gqc
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Oxidoreductase
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PDB id
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4gqc
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PDB id:
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| Name: |
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Oxidoreductase
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Title:
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Crystal structure of aeropyrum pernix peroxiredoxin q enzyme in fully- folded and locally-unfolded conformations
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Structure:
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Thiol peroxidase. Chain: a, b, c, d. Synonym: peroxiredoxin q. Engineered: yes
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Source:
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Aeropyrum pernix. Organism_taxid: 272557. Strain: atcc 700893 / dsm 11879 / jcm 9820 / nbrc 100138 / k1. Gene: ape2125, ape_2125.1, bcp. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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2.00Å
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R-factor:
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0.197
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R-free:
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0.235
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Authors:
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A.Perkins,P.A.Karplus,M.C.Gretes,K.J.Nelson,L.B.Poole
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Key ref:
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A.Perkins
et al.
(2012).
Mapping the active site helix-to-strand conversion of CxxxxC peroxiredoxin Q enzymes.
Biochemistry,
51,
7638-7650.
PubMed id:
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Date:
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22-Aug-12
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Release date:
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24-Oct-12
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PROCHECK
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Headers
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References
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Q9YA14
(Q9YA14_AERPE) -
Thiol peroxidase from Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
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Seq:
Struc:
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161 a.a.
160 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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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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Enzyme class:
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E.C.1.11.1.15
- Transferred entry: 1.11.1.24, 1.11.1.25, 1.11.1.26, 1.11.1.27, 1.11.1.28
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Pathway:
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Peroxiredoxin
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Reaction:
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2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH
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2
×
R'-SH
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+
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ROOH
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=
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R'-S-S-R'
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+
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H(2)O
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+
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ROH
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Biochemistry
51:7638-7650
(2012)
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PubMed id:
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Mapping the active site helix-to-strand conversion of CxxxxC peroxiredoxin Q enzymes.
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A.Perkins,
M.C.Gretes,
K.J.Nelson,
L.B.Poole,
P.A.Karplus.
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ABSTRACT
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Peroxiredoxins (Prx) make up a family of enzymes that reduce peroxides using a
peroxidatic cysteine residue; among these, members of the PrxQ subfamily are
proposed to be the most ancestral-like yet are among the least characterized. In
many PrxQ enzymes, a second "resolving" cysteine is located five
residues downstream from the peroxidatic Cys, and these residues form a
disulfide during the catalytic cycle. Here, we describe three hyperthermophilic
PrxQ crystal structures originally determined by the RIKEN structural genomics
group. We reprocessed the diffraction data and conducted further refinement to
yield models with R(free) values lowered by 2.3-7.2% and resolution extended by
0.2-0.3 Å, making one, at 1.4 Å, one of the best resolved peroxiredoxins to
date. Comparisons of two matched thiol and disulfide forms reveal that the
active site conformational change required for disulfide formation involves a
transition of ∼20 residues from a pair of α-helices to a β-hairpin and
3(10)-helix. Each conformation has ∼10 residues with a high level of disorder
providing slack that allows the dramatic shift, and the two conformations are
anchored to the protein core by distinct nonpolar side chains that fill three
hydrophobic pockets. Sequence conservation patterns confirm the importance of
these and a few additional residues for function. From a broader perspective,
this study raises the provocative question of how to make use of the valuable
information in the Protein Data Bank generated by structural genomics projects
but not described in the literature, perhaps remaining unrecognized and
certainly underutilized.
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