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PDBsum entry 3zjs
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Iron-binding protein
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PDB id
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3zjs
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PDB id:
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| Name: |
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Iron-binding protein
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Title:
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M.Acetivorans protoglobin in complex with azide and xenon
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Structure:
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Protoglobin. Chain: a, b. Engineered: yes. Mutation: yes
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Source:
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Methanosarcina acetivorans. Organism_taxid: 2214. Expressed in: escherichia coli. Expression_system_taxid: 562
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Resolution:
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2.30Å
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R-factor:
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0.223
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R-free:
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0.274
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Authors:
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A.Pesce,L.Tilleman,J.Donne,E.Aste,P.Ascenzi,C.Ciaccio,M.Coletta, L.Moens,C.Viappiani,S.Dewilde,M.Bolognesi,M.Nardini
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Key ref:
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A.Pesce
et al.
(2013).
Structure and haem-distal site plasticity in Methanosarcina acetivorans protoglobin.
Plos One,
8,
e66144.
PubMed id:
DOI:
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Date:
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18-Jan-13
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Release date:
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26-Jun-13
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PROCHECK
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Headers
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References
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Q8TLY9
(Q8TLY9_METAC) -
Globin-sensor domain-containing protein from Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)
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Seq:
Struc:
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195 a.a.
191 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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DOI no:
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Plos One
8:e66144
(2013)
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PubMed id:
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Structure and haem-distal site plasticity in Methanosarcina acetivorans protoglobin.
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A.Pesce,
L.Tilleman,
J.Donné,
E.Aste,
P.Ascenzi,
C.Ciaccio,
M.Coletta,
L.Moens,
C.Viappiani,
S.Dewilde,
M.Bolognesi,
M.Nardini.
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ABSTRACT
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Protoglobin from Methanosarcina acetivorans C2A (MaPgb), a strictly anaerobic
methanogenic Archaea, is a dimeric haem-protein whose biological role is still
unknown. As other globins, protoglobin can bind O2, CO and NO reversibly in
vitro, but it displays specific functional and structural properties within
members of the hemoglobin superfamily. CO binding to and dissociation from the
haem occurs through biphasic kinetics, which arise from binding to (and
dissociation from) two distinct tertiary states in a ligation-dependent
equilibrium. From the structural viewpoint, protoglobin-specific loops and a
N-terminal extension of 20 residues completely bury the haem within the protein
matrix. Thus, access of small ligand molecules to the haem is granted by two
apolar tunnels, not common to other globins, which reach the haem distal site
from locations at the B/G and B/E helix interfaces. Here, the roles played by
residues Trp(60)B9, Tyr(61)B10 and Phe(93)E11 in ligand recognition and
stabilization are analyzed, through crystallographic investigations on the
ferric protein and on selected mutants. Specifically, protein structures are
reported for protoglobin complexes with cyanide, with azide (also in the
presence of Xenon), and with more bulky ligands, such as imidazole and
nicotinamide. Values of the rate constant for cyanide dissociation from ferric
MaPgb-cyanide complexes have been correlated to hydrogen bonds provided by
Trp(60)B9 and Tyr(61)B10 that stabilize the haem-Fe(III)-bound cyanide. We show
that protoglobin can strikingly reshape, in a ligand-dependent way, the haem
distal site, where Phe(93)E11 acts as ligand sensor and controls accessibility
to the haem through the tunnel system by modifying the conformation of Trp(60)B9.
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Links
