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PDBsum entry 2qyg
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Unknown function
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PDB id
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2qyg
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Contents |
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* Residue conservation analysis
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PDB id:
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Unknown function
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Title:
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Crystal structure of a rubisco-like protein rlp2 from rhodopseudomonas palustris
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Structure:
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Ribulose bisphosphate carboxylase-like protein 2. Chain: a, b, c, d. Synonym: rubisco-like protein. Engineered: yes
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Source:
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Rhodopseudomonas palustris. Organism_taxid: 258594. Strain: cga009. Gene: rlp2. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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3.30Å
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R-factor:
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0.204
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R-free:
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0.232
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Authors:
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H.Li,S.Chan,F.R.Tabita,D.Eisenberg
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Key ref:
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F.R.Tabita
et al.
(2007).
Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs.
Microbiol Mol Biol Rev,
71,
576-599.
PubMed id:
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Date:
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14-Aug-07
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Release date:
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11-Sep-07
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PROCHECK
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Headers
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References
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Q6ND47
(RBLL2_RHOPA) -
Ribulose bisphosphate carboxylase-like protein 2 from Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
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Seq:
Struc:
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432 a.a.
429 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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Microbiol Mol Biol Rev
71:576-599
(2007)
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PubMed id:
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Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs.
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F.R.Tabita,
T.E.Hanson,
H.Li,
S.Satagopan,
J.Singh,
S.Chan.
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ABSTRACT
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About 30 years have now passed since it was discovered that microbes synthesize
RubisCO molecules that differ from the typical plant paradigm. RubisCOs of forms
I, II, and III catalyze CO(2) fixation reactions, albeit for potentially
different physiological purposes, while the RubisCO-like protein (RLP) (form IV
RubisCO) has evolved, thus far at least, to catalyze reactions that are
important for sulfur metabolism. RubisCO is the major global CO(2) fixation
catalyst, and RLP is a somewhat related protein, exemplified by the fact that
some of the latter proteins, along with RubisCO, catalyze similar enolization
reactions as a part of their respective catalytic mechanisms. RLP in some
organisms catalyzes a key reaction of a methionine salvage pathway, while in
green sulfur bacteria, RLP plays a role in oxidative thiosulfate metabolism. In
many organisms, the function of RLP is unknown. Indeed, there now appear to be
at least six different clades of RLP molecules found in nature. Consideration of
the many RubisCO (forms I, II, and III) and RLP (form IV) sequences in the
database has subsequently led to a coherent picture of how these proteins may
have evolved, with a form III RubisCO arising from the Methanomicrobia as the
most likely ultimate source of all RubisCO and RLP lineages. In addition,
structure-function analyses of RLP and RubisCO have provided information as to
how the active sites of these proteins have evolved for their specific functions.
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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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A.Bracher,
A.Starling-Windhof,
F.U.Hartl,
and
M.Hayer-Hartl
(2011).
Crystal structure of a chaperone-bound assembly intermediate of form I Rubisco.
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Nat Struct Mol Biol,
18,
875-880.
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PDB code:
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A.Lykidis,
C.L.Chen,
S.G.Tringe,
A.C.McHardy,
A.Copeland,
N.C.Kyrpides,
P.Hugenholtz,
H.Macarie,
A.Olmos,
O.Monroy,
and
W.T.Liu
(2011).
Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium.
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ISME J,
5,
122-130.
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M.Hügler,
and
S.M.Sievert
(2011).
Beyond the Calvin cycle: autotrophic carbon fixation in the ocean.
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Ann Rev Mar Sci,
3,
261-289.
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O.L.Kovaleva,
T.P.Tourova,
G.Muyzer,
T.V.Kolganova,
and
D.Y.Sorokin
(2011).
Diversity of RuBisCO and ATP citrate lyase genes in soda lake sediments.
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FEMS Microbiol Ecol,
75,
37-47.
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B.Witte,
D.John,
B.Wawrik,
J.H.Paul,
D.Dayan,
and
F.R.Tabita
(2010).
Functional prokaryotic RubisCO from an oceanic metagenomic library.
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Appl Environ Microbiol,
76,
2997-3003.
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C.Liu,
A.L.Young,
A.Starling-Windhof,
A.Bracher,
S.Saschenbrecker,
B.V.Rao,
K.V.Rao,
O.Berninghausen,
T.Mielke,
F.U.Hartl,
R.Beckmann,
and
M.Hayer-Hartl
(2010).
Coupled chaperone action in folding and assembly of hexadecameric Rubisco.
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Nature,
463,
197-202.
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PDB codes:
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I.A.Berg,
D.Kockelkorn,
W.H.Ramos-Vera,
R.F.Say,
J.Zarzycki,
M.Hügler,
B.E.Alber,
and
G.Fuchs
(2010).
Autotrophic carbon fixation in archaea.
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Nat Rev Microbiol,
8,
447-460.
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J.Singh,
and
F.R.Tabita
(2010).
Roles of RubisCO and the RubisCO-like protein in 5-methylthioadenosine metabolism in the Nonsulfur purple bacterium Rhodospirillum rubrum.
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J Bacteriol,
192,
1324-1331.
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T.Barkay,
K.Kritee,
E.Boyd,
and
G.Geesey
(2010).
A thermophilic bacterial origin and subsequent constraints by redox, light and salinity on the evolution of the microbial mercuric reductase.
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Environ Microbiol,
12,
2904-2917.
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D.Wu,
J.Raymond,
M.Wu,
S.Chatterji,
Q.Ren,
J.E.Graham,
D.A.Bryant,
F.Robb,
A.Colman,
L.J.Tallon,
J.H.Badger,
R.Madupu,
N.L.Ward,
and
J.A.Eisen
(2009).
Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum.
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PLoS ONE,
4,
e4207.
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H.Tamura,
H.Ashida,
S.Koga,
Y.Saito,
T.Yadani,
Y.Kai,
T.Inoue,
A.Yokota,
and
H.Matsumura
(2009).
Crystallization and preliminary X-ray analysis of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
65,
147-150.
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H.Tamura,
Y.Saito,
H.Ashida,
Y.Kai,
T.Inoue,
A.Yokota,
and
H.Matsumura
(2009).
Structure of the apo decarbamylated form of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis.
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Acta Crystallogr D Biol Crystallogr,
65,
942-951.
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PDB code:
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J.H.Lee,
D.O.Park,
S.W.Park,
E.H.Hwang,
J.I.Oh,
and
Y.M.Kim
(2009).
Expression and regulation of ribulose 1,5-bisphosphate carboxylase/oxygenase genes in Mycobacterium sp. strain JC1 DSM 3803.
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J Microbiol,
47,
297-307.
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J.S.Blum,
S.Han,
B.Lanoil,
C.Saltikov,
B.Witte,
F.R.Tabita,
S.Langley,
T.J.Beveridge,
L.Jahnke,
and
R.S.Oremland
(2009).
Ecophysiology of "Halarsenatibacter silvermanii" strain SLAS-1T, gen. nov., sp. nov., a facultative chemoautotrophic arsenate respirer from salt-saturated Searles Lake, California.
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Appl Environ Microbiol,
75,
1950-1960.
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O.Zhaxybayeva,
K.S.Swithers,
P.Lapierre,
G.P.Fournier,
D.M.Bickhart,
R.T.DeBoy,
K.E.Nelson,
C.L.Nesbø,
W.F.Doolittle,
J.P.Gogarten,
and
K.M.Noll
(2009).
On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales.
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Proc Natl Acad Sci U S A,
106,
5865-5870.
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S.Satagopan,
S.S.Scott,
T.G.Smith,
and
F.R.Tabita
(2009).
A Rubisco mutant that confers growth under a normally "inhibitory" oxygen concentration.
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Biochemistry,
48,
9076-9083.
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Y.Saito,
H.Ashida,
T.Sakiyama,
N.T.de Marsac,
A.Danchin,
A.Sekowska,
and
A.Yokota
(2009).
Structural and functional similarities between a ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)-like protein from Bacillus subtilis and photosynthetic RuBisCO.
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J Biol Chem,
284,
13256-13264.
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F.R.Tabita,
T.E.Hanson,
S.Satagopan,
B.H.Witte,
and
N.E.Kreel
(2008).
Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms.
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Philos Trans R Soc Lond B Biol Sci,
363,
2629-2640.
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G.Levicán,
J.A.Ugalde,
N.Ehrenfeld,
A.Maass,
and
P.Parada
(2008).
Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations.
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BMC Genomics,
9,
581.
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H.J.Imker,
J.Singh,
B.P.Warlick,
F.R.Tabita,
and
J.A.Gerlt
(2008).
Mechanistic diversity in the RuBisCO superfamily: a novel isomerization reaction catalyzed by the RuBisCO-like protein from Rhodospirillum rubrum.
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Biochemistry,
47,
11171-11173.
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J.M.Norton,
M.G.Klotz,
L.Y.Stein,
D.J.Arp,
P.J.Bottomley,
P.S.Chain,
L.J.Hauser,
M.L.Land,
F.W.Larimer,
M.W.Shin,
and
S.R.Starkenburg
(2008).
Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment.
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Appl Environ Microbiol,
74,
3559-3572.
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M.Mentel,
and
W.Martin
(2008).
Energy metabolism among eukaryotic anaerobes in light of Proterozoic ocean chemistry.
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Philos Trans R Soc Lond B Biol Sci,
363,
2717-2729.
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S.Nakagawa,
and
K.Takai
(2008).
Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance.
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FEMS Microbiol Ecol,
65,
1.
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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
code is
shown on the right.
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Links
