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PDBsum entry 1e5d
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Oxidoreductase
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PDB id
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1e5d
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Contents |
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* Residue conservation analysis
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PDB id:
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Oxidoreductase
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Title:
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Rubredoxin oxygen:oxidoreductase (roo) from anaerobe desulfovibrio gigas
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Structure:
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Rubredoxin\:oxygen oxidoreductase. Chain: a, b
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Source:
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Desulfovibrio gigas. Organism_taxid: 879
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Biol. unit:
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Homo-Dimer (from PDB file)
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Resolution:
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2.50Å
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R-factor:
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0.179
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R-free:
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0.248
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Authors:
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C.Frazao,G.Silva,C.M.Gomes,P.Matias,R.Coelho,L.Sieker,S.Macedo, M.Y.Liu,S.Oliveira,M.Teixeira,A.V.Xavier,C.Rodrigues-Pousada, M.A.Carrondo,J.Le Gall
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Key ref:
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C.Frazão
et al.
(2000).
Structure of a dioxygen reduction enzyme from Desulfovibrio gigas.
Nat Struct Biol,
7,
1041-1045.
PubMed id:
DOI:
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Date:
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24-Jul-00
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Release date:
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17-Nov-00
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PROCHECK
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Headers
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References
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Q9F0J6
(ROO_MEGG1) -
Rubredoxin-oxygen oxidoreductase from Megalodesulfovibrio gigas (strain ATCC 19364 / DSM 1382 / NCIMB 9332 / VKM B-1759)
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Seq:
Struc:
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402 a.a.
401 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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DOI no:
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Nat Struct Biol
7:1041-1045
(2000)
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PubMed id:
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Structure of a dioxygen reduction enzyme from Desulfovibrio gigas.
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C.Frazão,
G.Silva,
C.M.Gomes,
P.Matias,
R.Coelho,
L.Sieker,
S.Macedo,
M.Y.Liu,
S.Oliveira,
M.Teixeira,
A.V.Xavier,
C.Rodrigues-Pousada,
M.A.Carrondo,
J.Le Gall.
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ABSTRACT
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Desulfovibrio gigas is a strict anaerobe that contains a well-characterized
metabolic pathway that enables it to survive transient contacts with oxygen. The
terminal enzyme in this pathway, rubredoxin:oxygen oxidoreductase (ROO) reduces
oxygen to water in a direct and safe way. The 2.5 A resolution crystal structure
of ROO shows that each monomer of this homodimeric enzyme consists of a novel
combination of two domains, a flavodoxin-like domain and a
Zn-beta-lactamase-like domain that contains a di-iron center for dioxygen
reduction. This is the first structure of a member of a superfamily of enzymes
widespread in strict and facultative anaerobes, indicating its broad
physiological significance.
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Selected figure(s)
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Figure 2.
Figure 2. ROO is a modular enzyme. a, The ROO dimer (monomers
in blue and brown), showing the  -lactamase-like
(light) and flavodoxin-like (dark) domains, iron (orange
spheres) and FMN (stick model). A two-fold axis relates both
monomers. b, The -lactamase-like
domain. Left, a ribbon diagram with termini labeled. Right,
stereo view of the -lactamase-like
domain (blue) superimposed on -lactamases
from Stenotrophomonas maltophilia^11 (green), Bacillus cereus12
(deep pink) and Bacteroides fragilis13 (gold). Additional ROO
structural elements in the region corresponding to the substrate
groove of -lactamases
are indicated in dark blue. c, The flavodoxin-like domain. Left,
ribbon diagram. Right, stereo view of the flavodoxin-like domain
(blue) superimposed on Desulfovibrio vulgaris 32 (brown) and
Clostridium beijerinckii17 (violet) flavodoxins.
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Figure 3.
Figure 3. 3 ROO catalytic site. a, Distances (Å) are given
for contacts to the pentacoordinated (quadrangular pyramid) Fe 1
and tetracoordinated (quadrangular plane) Fe 2 coordinations
(green), and for other close contacts (cyan). The oxygen
molecule (OXY) and water (WAT 1) are close to Fe 2, but outside
the typical bonding distances. Similar to other di-iron
proteins14, 15, this site contains a bridging  -O
(or -OH;
MUO) at hydrogen bonding distance from the Asp 83 OD1. The
electron density was contoured at 1  (blue)
and 7 (red).
b, ROO dimerization (monomers in blue and brown) couples the two
monomer cofactors. The spatial orientations of the side chains
of His 79, Glu 81, and His 226 are stabilized through hydrogen
bonds to the side chains of Asp 149 and Trp 263 and to the
carbonyl O of Tyr 34, respectively. Intradimer contacts involve
Trp 147, Pro 148 and Asp 149 as well as the aromatic ring of Trp
347.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2000,
7,
1041-1045)
copyright 2000.
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Figures were
selected
by an automated process.
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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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M.L.Wu,
S.de Vries,
T.A.van Alen,
M.K.Butler,
H.J.Op den Camp,
J.T.Keltjens,
M.S.Jetten,
and
M.Strous
(2011).
Physiological role of the respiratory quinol oxidase in the anaerobic nitrite-reducing methanotroph 'Candidatus Methylomirabilis oxyfera'.
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Microbiology,
157,
890-898.
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V.L.Gonçalves,
L.M.Saraiva,
and
M.Teixeira
(2011).
Gene expression study of the flavodi-iron proteins from the cyanobacterium Synechocystis sp. PCC6803.
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Biochem Soc Trans,
39,
216-218.
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A.L.Stamp,
P.Owen,
K.E.Omari,
C.E.Nichols,
M.Lockyer,
H.K.Lamb,
I.G.Charles,
A.R.Hawkins,
and
D.K.Stammers
(2010).
Structural and functional characterization of Salmonella enterica serovar Typhimurium YcbL: an unusual Type II glyoxalase.
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Protein Sci,
19,
1897-1905.
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PDB code:
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V.A.Campos-Bermudez,
J.Morán-Barrio,
A.J.Costa-Filho,
and
A.J.Vila
(2010).
Metal-dependent inhibition of glyoxalase II: a possible mechanism to regulate the enzyme activity.
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J Inorg Biochem,
104,
726-731.
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B.L.Victor,
A.M.Baptista,
and
C.M.Soares
(2009).
Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:oxygen oxidoreductase from Desulfovibrio gigas.
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J Biol Inorg Chem,
14,
853-862.
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C.Hackenberg,
A.Engelhardt,
H.C.Matthijs,
F.Wittink,
H.Bauwe,
A.Kaplan,
and
M.Hagemann
(2009).
Photorespiratory 2-phosphoglycolate metabolism and photoreduction of O2 cooperate in high-light acclimation of Synechocystis sp. strain PCC 6803.
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Planta,
230,
625-637.
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F.Hillmann,
O.Riebe,
R.J.Fischer,
A.Mot,
J.D.Caranto,
D.M.Kurtz,
and
H.Bahl
(2009).
Reductive dioxygen scavenging by flavo-diiron proteins of Clostridium acetobutylicum.
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FEBS Lett,
583,
241-245.
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P.Limphong,
M.W.Crowder,
B.Bennett,
and
C.A.Makaroff
(2009).
Arabidopsis thaliana GLX2-1 contains a dinuclear metal binding site, but is not a glyoxalase 2.
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Biochem J,
417,
323-330.
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P.Zhang,
Y.Allahverdiyeva,
M.Eisenhut,
and
E.M.Aro
(2009).
Flavodiiron proteins in oxygenic photosynthetic organisms: photoprotection of photosystem II by Flv2 and Flv4 in Synechocystis sp. PCC 6803.
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PLoS ONE,
4,
e5331.
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T.Smutná,
V.L.Gonçalves,
L.M.Saraiva,
J.Tachezy,
M.Teixeira,
and
I.Hrdy
(2009).
Flavodiiron protein from Trichomonas vaginalis hydrogenosomes: the terminal oxygen reductase.
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Eukaryot Cell,
8,
47-55.
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A.Di Matteo,
F.M.Scandurra,
F.Testa,
E.Forte,
P.Sarti,
M.Brunori,
and
A.Giuffrè
(2008).
The O2-scavenging flavodiiron protein in the human parasite Giardia intestinalis.
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J Biol Chem,
283,
4061-4068.
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PDB code:
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A.Yamamura,
J.Ohtsuka,
K.Kubota,
Y.Agari,
A.Ebihara,
N.Nakagawa,
K.Nagata,
and
M.Tanokura
(2008).
Crystal structure of TTHA1429, a novel metallo-beta-lactamase superfamily protein from Thermus thermophilus HB8.
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Proteins,
73,
1053-1057.
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PDB code:
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C.Le Fourn,
M.L.Fardeau,
B.Ollivier,
E.Lojou,
and
A.Dolla
(2008).
The hyperthermophilic anaerobe Thermotoga Maritima is able to cope with limited amount of oxygen: insights into its defence strategies.
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Environ Microbiol,
10,
1877-1887.
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M.M.Holdorf,
B.Bennett,
M.W.Crowder,
and
C.A.Makaroff
(2008).
Spectroscopic studies on Arabidopsis ETHE1, a glyoxalase II-like protein.
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J Inorg Biochem,
102,
1825-1830.
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M.V.Petoukhov,
J.B.Vicente,
P.B.Crowley,
M.A.Carrondo,
M.Teixeira,
and
D.I.Svergun
(2008).
Quaternary structure of flavorubredoxin as revealed by synchrotron radiation small-angle X-ray scattering.
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Structure,
16,
1428-1436.
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C.H.Tung,
J.W.Huang,
and
J.M.Yang
(2007).
Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database.
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Genome Biol,
8,
R31.
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G.Hagelueken,
L.Wiehlmann,
T.M.Adams,
H.Kolmar,
D.W.Heinz,
B.Tümmler,
and
W.D.Schubert
(2007).
Crystal structure of the electron transfer complex rubredoxin rubredoxin reductase of Pseudomonas aeruginosa.
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Proc Natl Acad Sci U S A,
104,
12276-12281.
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PDB codes:
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H.Seedorf,
C.H.Hagemeier,
S.Shima,
R.K.Thauer,
E.Warkentin,
and
U.Ermler
(2007).
Structure of coenzyme F420H2 oxidase (FprA), a di-iron flavoprotein from methanogenic Archaea catalyzing the reduction of O2 to H2O.
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FEBS J,
274,
1588-1599.
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PDB codes:
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J.B.Vicente,
F.M.Scandurra,
J.V.Rodrigues,
M.Brunori,
P.Sarti,
M.Teixeira,
and
A.Giuffrè
(2007).
Kinetics of electron transfer from NADH to the Escherichia coli nitric oxide reductase flavorubredoxin.
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FEBS J,
274,
677-686.
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K.S.Bender,
H.C.Yen,
C.L.Hemme,
Z.Yang,
Z.He,
Q.He,
J.Zhou,
K.H.Huang,
E.J.Alm,
T.C.Hazen,
A.P.Arkin,
and
J.D.Wall
(2007).
Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough.
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Appl Environ Microbiol,
73,
5389-5400.
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M.A.Carrondo,
I.Bento,
P.M.Matias,
and
P.F.Lindley
(2007).
Crystallographic evidence for dioxygen interactions with iron proteins.
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J Biol Inorg Chem,
12,
429-442.
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Y.Okamoto,
J.Wang,
J.Morishita,
and
N.Ueda
(2007).
Biosynthetic pathways of the endocannabinoid anandamide.
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Chem Biodivers,
4,
1842-1857.
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G.Hagelueken,
T.M.Adams,
L.Wiehlmann,
U.Widow,
H.Kolmar,
B.Tümmler,
D.W.Heinz,
and
W.D.Schubert
(2006).
The crystal structure of SdsA1, an alkylsulfatase from Pseudomonas aeruginosa, defines a third class of sulfatases.
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Proc Natl Acad Sci U S A,
103,
7631-7636.
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PDB codes:
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J.D.Wildschut,
R.M.Lang,
J.K.Voordouw,
and
G.Voordouw
(2006).
Rubredoxin:oxygen oxidoreductase enhances survival of Desulfovibrio vulgaris hildenborough under microaerophilic conditions.
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J Bacteriol,
188,
6253-6260.
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J.E.Guy,
I.A.Abreu,
M.Moche,
Y.Lindqvist,
E.Whittle,
and
J.Shanklin
(2006).
A single mutation in the castor Delta9-18:0-desaturase changes reaction partitioning from desaturation to oxidase chemistry.
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Proc Natl Acad Sci U S A,
103,
17220-17224.
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PDB code:
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J.Wang,
Y.Okamoto,
J.Morishita,
K.Tsuboi,
A.Miyatake,
and
N.Ueda
(2006).
Functional analysis of the purified anandamide-generating phospholipase D as a member of the metallo-beta-lactamase family.
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J Biol Chem,
281,
12325-12335.
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P.Machado,
R.Félix,
R.Rodrigues,
S.Oliveira,
and
C.Rodrigues-Pousada
(2006).
Characterization and expression analysis of the cytochrome bd oxidase operon from Desulfovibrio gigas.
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Curr Microbiol,
52,
274-281.
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R.Agarwal,
J.B.Bonanno,
S.K.Burley,
and
S.Swaminathan
(2006).
Structure determination of an FMN reductase from Pseudomonas aeruginosa PA01 using sulfur anomalous signal.
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Acta Crystallogr D Biol Crystallogr,
62,
383-391.
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PDB codes:
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R.Rodrigues,
J.B.Vicente,
R.Félix,
S.Oliveira,
M.Teixeira,
and
C.Rodrigues-Pousada
(2006).
Desulfovibrio gigas flavodiiron protein affords protection against nitrosative stress in vivo.
|
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J Bacteriol,
188,
2745-2751.
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A.Vogel,
O.Schilling,
B.Späth,
and
A.Marchfelder
(2005).
The tRNase Z family of proteins: physiological functions, substrate specificity and structural properties.
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Biol Chem,
386,
1253-1264.
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D.Liu,
B.W.Lepore,
G.A.Petsko,
P.W.Thomas,
E.M.Stone,
W.Fast,
and
D.Ringe
(2005).
Three-dimensional structure of the quorum-quenching N-acyl homoserine lactone hydrolase from Bacillus thuringiensis.
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Proc Natl Acad Sci U S A,
102,
11882-11887.
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PDB code:
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G.Garau,
A.M.Di Guilmi,
and
B.G.Hall
(2005).
Structure-based phylogeny of the metallo-beta-lactamases.
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Antimicrob Agents Chemother,
49,
2778-2784.
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G.Garau,
D.Lemaire,
T.Vernet,
O.Dideberg,
and
A.M.Di Guilmi
(2005).
Crystal structure of phosphorylcholine esterase domain of the virulence factor choline-binding protein e from streptococcus pneumoniae: new structural features among the metallo-beta-lactamase superfamily.
|
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J Biol Chem,
280,
28591-28600.
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PDB codes:
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G.P.Marasinghe,
I.M.Sander,
B.Bennett,
G.Periyannan,
K.W.Yang,
C.A.Makaroff,
and
M.W.Crowder
(2005).
Structural studies on a mitochondrial glyoxalase II.
|
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J Biol Chem,
280,
40668-40675.
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PDB code:
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I.L.de la Sierra-Gallay,
O.Pellegrini,
and
C.Condon
(2005).
Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z.
|
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Nature,
433,
657-661.
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PDB code:
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J.A.Hermoso,
L.Lagartera,
A.González,
M.Stelter,
P.García,
M.Martínez-Ripoll,
J.L.García,
and
M.Menéndez
(2005).
Insights into pneumococcal pathogenesis from the crystal structure of the modular teichoic acid phosphorylcholine esterase Pce.
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Nat Struct Mol Biol,
12,
533-538.
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PDB code:
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J.B.Vicente,
and
M.Teixeira
(2005).
Redox and spectroscopic properties of the Escherichia coli nitric oxide-detoxifying system involving flavorubredoxin and its NADH-oxidizing redox partner.
|
| |
J Biol Chem,
280,
34599-34608.
|
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J.Gorman,
and
L.Shapiro
(2005).
Crystal structures of the tryptophan repressor binding protein WrbA and complexes with flavin mononucleotide.
|
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Protein Sci,
14,
3004-3012.
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PDB codes:
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L.Lagartera,
A.González,
J.A.Hermoso,
J.L.Saíz,
P.García,
J.L.García,
and
M.Menéndez
(2005).
Pneumococcal phosphorylcholine esterase, Pce, contains a metal binuclear center that is essential for substrate binding and catalysis.
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Protein Sci,
14,
3013-3024.
|
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O.Schilling,
B.Späth,
B.Kostelecky,
A.Marchfelder,
W.Meyer-Klaucke,
and
A.Vogel
(2005).
Exosite modules guide substrate recognition in the ZiPD/ElaC protein family.
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| |
J Biol Chem,
280,
17857-17862.
|
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S.L.Andrade,
F.Cruz,
C.L.Drennan,
V.Ramakrishnan,
D.C.Rees,
J.G.Ferry,
and
O.Einsle
(2005).
Structures of the iron-sulfur flavoproteins from Methanosarcina thermophila and Archaeoglobus fulgidus.
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J Bacteriol,
187,
3848-3854.
|
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|
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S.S.Leal,
and
C.M.Gomes
(2005).
Linear three-iron centres are unlikely cluster degradation intermediates during unfolding of iron-sulfur proteins.
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| |
Biol Chem,
386,
1295-1300.
|
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D.A.Rodionov,
I.Dubchak,
A.Arkin,
E.Alm,
and
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Where a reference describes a PDB structure, the PDB
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