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PDBsum entry 1ebc
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* Residue conservation analysis
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Enzyme class 2:
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E.C.1.11.1.-
- ?????
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Enzyme class 3:
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E.C.1.7.-.-
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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Biophys J
77:1093-1099
(1999)
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PubMed id:
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Cyanide binding to Lucina pectinata hemoglobin I and to sperm whale myoglobin: an x-ray crystallographic study.
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M.Bolognesi,
C.Rosano,
R.Losso,
A.Borassi,
M.Rizzi,
J.B.Wittenberg,
A.Boffi,
P.Ascenzi.
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ABSTRACT
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The x-ray crystal structures of the cyanide derivative of Lucina pectinata
monomeric hemoglobin I (L. pectinata HbI) and sperm whale (Physeter catodon)
myoglobin (Mb), generally taken as reference models for monomeric hemoproteins
carrying hydrogen sulfide and oxygen, respectively, have been determined at 1.9
A (R-factor = 0. 184), and 1.8 A (R-factor = 0.181) resolution, respectively, at
room temperature (lambda = 1.542 A). Moreover, the x-ray crystal structure of
the L. pectinata HbI:cyanide derivative has been studied at 1.4-A resolution
(R-factor = 0.118) and 100 K (on a synchrotron source lambda = 0.998 A). At room
temperature, the cyanide ligand is roughly parallel to the heme plane of L.
pectinata HbI, being located approximately 2.5 A from the iron atom. On the
other hand, the crystal structure of the L. pectinata HbI:cyanide derivative at
100 K shows that the diatomic ligand is coordinated to the iron atom in an
orientation almost perpendicular to the heme (the Fe-C distance being 1.95 A),
adopting a coordination geometry strictly reminescent of that observed in sperm
whale Mb, at room temperature. The unusual cyanide distal site orientation
observed in L. pectinata HbI, at room temperature, may reflect reduction of the
heme Fe(III) atom induced by free radical species during x-ray data collection
using Cu Kalpha radiation.
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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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V.S.de Serrano,
M.F.Davis,
J.F.Gaff,
Q.Zhang,
Z.Chen,
E.L.D'Antonio,
E.F.Bowden,
R.Rose,
and
S.Franzen
(2010).
X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: evidence for photoreductive dissociation of the iron-cyanide bond.
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Acta Crystallogr D Biol Crystallogr,
66,
770-782.
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PDB codes:
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C.R.Ruiz-Martínez,
C.A.Nieves-Marrero,
R.A.Estremera-Andújar,
J.A.Gavira,
L.A.González-Ramírez,
J.López-Garriga,
and
J.M.García-Ruiz
(2009).
Crystallization and diffraction patterns of the oxy and cyano forms of the Lucina pectinata haemoglobins complex.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
65,
25-28.
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J.A.Doebbler,
and
R.B.Von Dreele
(2009).
Application of molecular replacement to protein powder data from image plates.
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Acta Crystallogr D Biol Crystallogr,
65,
348-355.
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Y.Kung,
T.I.Doukov,
J.Seravalli,
S.W.Ragsdale,
and
C.L.Drennan
(2009).
Crystallographic snapshots of cyanide- and water-bound C-clusters from bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase.
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Biochemistry,
48,
7432-7440.
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PDB codes:
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A.Bolli,
C.Ciaccio,
M.Coletta,
M.Nardini,
M.Bolognesi,
A.Pesce,
M.Guertin,
P.Visca,
and
P.Ascenzi
(2008).
Ferrous Campylobacter jejuni truncated hemoglobin P displays an extremely high reactivity for cyanide - a comparative study.
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FEBS J,
275,
633-645.
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E.Ramirez,
A.Cruz,
D.Rodriguez,
L.Uchima,
R.Pietri,
A.Santana,
J.López-Garriga,
and
G.E.López
(2008).
Effects of active site mutations in haemoglobin I from Lucina pectinata: a molecular dynamic study.
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Mol Simul,
34,
715-725.
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J.A.Gavira,
A.Camara-Artigas,
W.De Jesús-Bonilla,
J.López-Garriga,
A.Lewis,
R.Pietri,
S.R.Yeh,
C.L.Cadilla,
and
J.M.García-Ruiz
(2008).
Structure and ligand selection of hemoglobin II from Lucina pectinata.
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J Biol Chem,
283,
9414-9423.
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PDB code:
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A.Arcovito,
M.Benfatto,
M.Cianci,
S.S.Hasnain,
K.Nienhaus,
G.U.Nienhaus,
C.Savino,
R.W.Strange,
B.Vallone,
and
S.Della Longa
(2007).
X-ray structure analysis of a metalloprotein with enhanced active-site resolution using in situ x-ray absorption near edge structure spectroscopy.
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Proc Natl Acad Sci U S A,
104,
6211-6216.
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PDB code:
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G.Battistuzzi,
M.Bellei,
L.Casella,
C.A.Bortolotti,
R.Roncone,
E.Monzani,
and
M.Sola
(2007).
Redox reactivity of the heme Fe3+/Fe 2+ couple in native myoglobins and mutants with peroxidase-like activity.
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J Biol Inorg Chem,
12,
951-958.
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J.Danielsson,
and
M.Meuwly
(2007).
Molecular dynamics simulations of CN- dynamics and spectroscopy in myoglobin.
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Chemphyschem,
8,
1077-1084.
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J.Li,
B.C.Noll,
C.E.Schulz,
and
W.R.Scheidt
(2007).
New insights on the electronic and molecular structure of cyanide-ligated iron(III) porphyrinates.
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Inorg Chem,
46,
2286-2298.
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M.Sugishima,
K.Oda,
T.Ogura,
H.Sakamoto,
M.Noguchi,
and
K.Fukuyama
(2007).
Alternative cyanide-binding modes to the haem iron in haem oxygenase.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
471-474.
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PDB code:
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V.de Serrano,
Z.Chen,
M.F.Davis,
and
S.Franzen
(2007).
X-ray crystal structural analysis of the binding site in the ferric and oxyferrous forms of the recombinant heme dehaloperoxidase cloned from Amphitrite ornata.
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Acta Crystallogr D Biol Crystallogr,
63,
1094-1101.
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PDB codes:
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M.D.Clay,
T.C.Yang,
F.E.Jenney,
I.Y.Kung,
C.A.Cosper,
R.Krishnan,
D.M.Kurtz,
M.W.Adams,
B.M.Hoffman,
and
M.K.Johnson
(2006).
Geometries and electronic structures of cyanide adducts of the non-heme iron active site of superoxide reductases: vibrational and ENDOR studies.
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Biochemistry,
45,
427-438.
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M.Nardini,
A.Pesce,
M.Labarre,
C.Richard,
A.Bolli,
P.Ascenzi,
M.Guertin,
and
M.Bolognesi
(2006).
Structural determinants in the group III truncated hemoglobin from Campylobacter jejuni.
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J Biol Chem,
281,
37803-37812.
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PDB code:
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S.Fernandez-Alberti,
D.E.Bacelo,
R.C.Binning,
J.Echave,
M.Chergui,
and
J.Lopez-Garriga
(2006).
Sulfide-binding hemoglobins: Effects of mutations on active-site flexibility.
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Biophys J,
91,
1698-1709.
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G.Battistuzzi,
M.Bellei,
M.Borsari,
G.Di Rocco,
A.Ranieri,
and
M.Sola
(2005).
Axial ligation and polypeptide matrix effects on the reduction potential of heme proteins probed on their cyanide adducts.
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J Biol Inorg Chem,
10,
643-651.
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M.Milani,
P.Y.Savard,
H.Ouellet,
P.Ascenzi,
M.Guertin,
and
M.Bolognesi
(2003).
A TyrCD1/TrpG8 hydrogen bond network and a TyrB10TyrCD1 covalent link shape the heme distal site of Mycobacterium tuberculosis hemoglobin O.
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Proc Natl Acad Sci U S A,
100,
5766-5771.
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PDB code:
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A.Pesce,
M.Nardini,
S.Dewilde,
E.Geuens,
K.Yamauchi,
P.Ascenzi,
A.F.Riggs,
L.Moens,
and
M.Bolognesi
(2002).
The 109 residue nerve tissue minihemoglobin from Cerebratulus lacteus highlights striking structural plasticity of the alpha-helical globin fold.
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Structure,
10,
725-735.
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PDB code:
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H.J.Park,
C.Yang,
N.Treff,
J.D.Satterlee,
and
C.Kang
(2002).
Crystal structures of unligated and CN-ligated Glycera dibranchiata monomer ferric hemoglobin components III and IV.
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Proteins,
49,
49-60.
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PDB codes:
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A.Pesce,
M.Couture,
S.Dewilde,
M.Guertin,
K.Yamauchi,
P.Ascenzi,
L.Moens,
and
M.Bolognesi
(2000).
A novel two-over-two alpha-helical sandwich fold is characteristic of the truncated hemoglobin family.
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EMBO J,
19,
2424-2434.
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PDB codes:
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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
