 |
PDBsum entry 1ux9
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Oxygen transport
|
PDB id
|
|
|
|
1ux9
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
PDB id:
|
|
|
|
| Name: |
|
Oxygen transport
|
|
|
Title:
|
|
Mapping protein matrix cavities in human cytoglobin through xe atom binding: a crystallographic investigation
|
|
Structure:
|
|
Cytoglobin. Chain: a, b. Synonym: histoglobin, hgb, stellate cell activation-associated- protein, cygb, stap. Engineered: yes. Mutation: yes
|
|
Source:
|
|
Homo sapiens. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562
|
|
Resolution:
|
|
|
2.40Å
|
R-factor:
|
0.194
|
R-free:
|
0.238
|
|
|
Authors:
|
|
D.De Sanctis,S.Dewilde,A.Pesce,L.Moens,P.Ascenzi,T.Hankeln, T.Burmester,M.Bolognesi
|
|
Key ref:
|
|
D.de Sanctis
et al.
(2004).
Mapping protein matrix cavities in human cytoglobin through Xe atom binding.
Biochem Biophys Res Commun,
316,
1217-1221.
PubMed id:
DOI:
|
|
|
Date:
|
|
|
23-Feb-04
|
Release date:
|
01-Jun-04
|
|
|
|
|
|
|
PROCHECK
|
|
|
|
|
|
Headers
|
|
|
|
References
|
|
|
|
|
|
|
|
Q8WWM9
(CYGB_HUMAN) -
Cytoglobin from Homo sapiens
|
|
|
|
Seq:
Struc:
|
|
|
|
190 a.a.
154 a.a.*
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Key: |
 |
PfamA domain |
|
|
 |
Secondary structure |
|
 |
CATH domain |
|
|
*
PDB and UniProt seqs differ
at 2 residue positions (black
crosses)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
DOI no:
|
Biochem Biophys Res Commun
316:1217-1221
(2004)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Mapping protein matrix cavities in human cytoglobin through Xe atom binding.
|
|
D.de Sanctis,
S.Dewilde,
A.Pesce,
L.Moens,
P.Ascenzi,
T.Hankeln,
T.Burmester,
M.Bolognesi.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Cytoglobin is the fourth recognized globin type, almost ubiquitously distributed
in human tissues; its function is still poorly understood. Cytoglobin displays a
core region of about 150 residues, structurally related to hemoglobin and
myoglobin, and two extra segments, about 20 residues each, at the N- and
C-termini. The core region hosts a large apolar cavity, held to provide a ligand
diffusion pathway to/from the heme, and/or ligand temporary docking sites. Here
we report the crystal structure (2.4A resolution, R-factor 19.1%) of a human
cytoglobin mutant bearing the CysB2(38) --> Ser and CysE9(83) --> Ser
substitutions (CYGB*), treated under pressurized xenon. Three Xe atoms bind to
the heme distal site region of CYGB* mapping the protein matrix apolar cavity.
Despite the conserved globin fold, the cavity found in CYGB* is structured
differently from those recognized to play a functional role in myoglobin,
neuroglobin, truncated hemoglobins, and Cerebratulus lacteus mini-hemoglobin.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
B.Zhang,
J.Xu,
Y.Li,
W.Du,
and
W.Fang
(2011).
Molecular dynamics simulation of carboxy and deoxy human cytoglobin in solution.
|
| |
J Inorg Biochem,
105,
949-956.
|
|
|
|
|
|
|
C.Savino,
A.E.Miele,
F.Draghi,
K.A.Johnson,
G.Sciara,
M.Brunori,
and
B.Vallone
(2009).
Pattern of cavities in globins: The case of human hemoglobin.
|
| |
Biopolymers,
91,
1097-1107.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
K.Teilum,
J.G.Olsen,
and
B.B.Kragelund
(2009).
Functional aspects of protein flexibility.
|
| |
Cell Mol Life Sci,
66,
2231-2247.
|
|
|
|
|
|
|
T.Moschetti,
U.Mueller,
J.Schulze,
M.Brunori,
and
B.Vallone
(2009).
The structure of neuroglobin at high Xe and Kr pressure reveals partial conservation of globin internal cavities.
|
| |
Biophys J,
97,
1700-1708.
|
|
|
|
|
|
|
L.Chen,
A.Y.Lyubimov,
L.Brammer,
A.Vrielink,
and
N.S.Sampson
(2008).
The binding and release of oxygen and hydrogen peroxide are directed by a hydrophobic tunnel in cholesterol oxidase.
|
| |
Biochemistry,
47,
5368-5377.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
L.Mouawad,
C.Tetreau,
S.Abdel-Azeim,
D.Perahia,
and
D.Lavalette
(2007).
CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations.
|
| |
Protein Sci,
16,
781-794.
|
|
|
|
|
|
|
S.Orlowski,
and
W.Nowak
(2007).
Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin.
|
| |
J Mol Model,
13,
715-723.
|
|
|
|
|
|
|
F.A.Walker
(2006).
The heme environment of mouse neuroglobin: histidine imidazole plane orientations obtained from solution NMR and EPR spectroscopy as compared with X-ray crystallography.
|
| |
J Biol Inorg Chem,
11,
391-397.
|
|
|
|
|
|
|
D.de Sanctis,
S.Dewilde,
C.Vonrhein,
A.Pesce,
L.Moens,
P.Ascenzi,
T.Hankeln,
T.Burmester,
M.Ponassi,
M.Nardini,
and
M.Bolognesi
(2005).
Bishistidyl heme hexacoordination, a key structural property in Drosophila melanogaster hemoglobin.
|
| |
J Biol Chem,
280,
27222-27229.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.Fago,
C.Hundahl,
S.Dewilde,
K.Gilany,
L.Moens,
and
R.E.Weber
(2004).
Allosteric regulation and temperature dependence of oxygen binding in human neuroglobin and cytoglobin. Molecular mechanisms and physiological significance.
|
| |
J Biol Chem,
279,
44417-44426.
|
|
|
|
|
|
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.
|
|
Links
