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PDBsum entry 1mjh
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Hypothetical protein
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PDB id
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1mjh
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Contents |
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* Residue conservation analysis
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PDB id:
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Hypothetical protein
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Title:
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Structure-based assignment of the biochemical function of hypothetical protein mj0577: a test case of structural genomics
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Structure:
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Protein (atp-binding domain of protein mj0577). Chain: a, b. Fragment: atp-binding domain. Engineered: yes. Other_details: complexed with adenosine-5'-triphosphate
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Source:
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Methanocaldococcus jannaschii. Organism_taxid: 2190. Cellular_location: cytoplasm. Gene: mj0577. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: recently sequenced hyperthermophile
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Biol. unit:
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Dimer (from
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Resolution:
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1.70Å
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R-factor:
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0.210
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R-free:
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0.254
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Authors:
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T.I.Zarembinski,L.-W.Hung,H.J.Mueller-Dieckmann,K.-K.Kim,H.Yokota, R.Kim,S.-H.Kim,Berkeley Structural Genomics Center (Bsgc)
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Key ref:
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T.I.Zarembinski
et al.
(1998).
Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics.
Proc Natl Acad Sci U S A,
95,
15189-15193.
PubMed id:
DOI:
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Date:
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04-Nov-98
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Release date:
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23-Dec-98
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PROCHECK
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Headers
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References
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Q57997
(Y577_METJA) -
Universal stress protein MJ0577 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
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Seq:
Struc:
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162 a.a.
143 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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Proc Natl Acad Sci U S A
95:15189-15193
(1998)
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PubMed id:
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Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics.
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T.I.Zarembinski,
L.W.Hung,
H.J.Mueller-Dieckmann,
K.K.Kim,
H.Yokota,
R.Kim,
S.H.Kim.
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ABSTRACT
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Many small bacterial, archaebacterial, and eukaryotic genomes have been
sequenced, and the larger eukaryotic genomes are predicted to be completely
sequenced within the next decade. In all genomes sequenced to date, a large
portion of these organisms' predicted protein coding regions encode polypeptides
of unknown biochemical, biophysical, and/or cellular functions.
Three-dimensional structures of these proteins may suggest biochemical or
biophysical functions. Here we report the crystal structure of one such protein,
MJ0577, from a hyperthermophile, Methanococcus jannaschii, at 1.7-A resolution.
The structure contains a bound ATP, suggesting MJ0577 is an ATPase or an
ATP-mediated molecular switch, which we confirm by biochemical experiments.
Furthermore, the structure reveals different ATP binding motifs that are shared
among many homologous hypothetical proteins in this family. This result
indicates that structure-based assignment of molecular function is a viable
approach for the large-scale biochemical assignment of proteins and for
discovering new motifs, a basic premise of structural genomics.
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Selected figure(s)
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Figure 2.
Fig. 2. Schematic drawing showing all of the hydrogen
bonds (dashed lines) involving ATP and coordination bonds
(dotted lines) involving the Mn+2 ion. The protein residues and
atoms involved in each hydrogen bond are shown in the boxes.
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Figure 3.
Fig. 3. Multiple alignment of conserved regions of the
MJ0577 superfamily showing four sequence motifs. It was
constructed by using PSI-BLAST (38) followed by CLUSTALW (39).
The first column shows the protein identifier with the letters
designating the organism code and the subsequent numbers
designating the gene. Organism codes: MJ, M. jannaschii; MTH,
Methanobacterium thermoautotrophicum; AF, Archaeoglobus
fulgidus; BS, Bacillus subtilis; AQ, Aquifex aeolicus. Conserved
residues are shaded. The black boxes below the sequence indicate
conserved residues contacting ATP (A: adenine; R: ribose; P:
phosphate; D: dimer interface).  -helices
and  -strands are
represented by brackets above the sequences. * at the C terminus
designate those sequences with tandem homologs of MJ0577.
Percent identities between the sequences are at far right.
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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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S.Forêt,
F.Seneca,
D.de Jong,
A.Bieller,
G.Hemmrich,
R.Augustin,
D.C.Hayward,
E.E.Ball,
T.C.Bosch,
K.Agata,
M.Hassel,
and
D.J.Miller
(2011).
Phylogenomics reveals an anomalous distribution of USP genes in metazoans.
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Mol Biol Evol,
28,
153-161.
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C.J.Shih,
and
M.C.Lai
(2010).
Differentially expressed genes after hyper- and hypo-salt stress in the halophilic archaeon Methanohalophilus portucalensis.
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Can J Microbiol,
56,
295-307.
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C.R.Shyu,
B.Pang,
P.H.Chi,
N.Zhao,
D.Korkin,
and
D.Xu
(2010).
ProteinDBS v2.0: a web server for global and local protein structure search.
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Nucleic Acids Res,
38,
W53-W58.
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S.M.Hingley-Wilson,
K.E.Lougheed,
K.Ferguson,
S.Leiva,
and
H.D.Williams
(2010).
Individual Mycobacterium tuberculosis universal stress protein homologues are dispensable in vitro.
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Tuberculosis (Edinb),
90,
236-244.
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W.T.Li,
Y.M.Wei,
J.R.Wang,
C.J.Liu,
X.J.Lan,
Q.T.Jiang,
Z.E.Pu,
and
Y.L.Zheng
(2010).
Identification, localization, and characterization of putative USP genes in barley.
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Theor Appl Genet,
121,
907-917.
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A.Edwards
(2009).
Large-scale structural biology of the human proteome.
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Annu Rev Biochem,
78,
541-568.
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J.E.Drumm,
K.Mi,
P.Bilder,
M.Sun,
J.Lim,
H.Bielefeldt-Ohmann,
R.Basaraba,
M.So,
G.Zhu,
J.M.Tufariello,
A.A.Izzo,
I.M.Orme,
S.C.Almo,
T.S.Leyh,
and
J.Chan
(2009).
Mycobacterium tuberculosis universal stress protein Rv2623 regulates bacillary growth by ATP-Binding: requirement for establishing chronic persistent infection.
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PLoS Pathog,
5,
e1000460.
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J.Gury,
H.Seraut,
N.P.Tran,
L.Barthelmebs,
S.Weidmann,
P.Gervais,
and
J.F.Cavin
(2009).
Inactivation of PadR, the repressor of the phenolic acid stress response, by molecular interaction with Usp1, a universal stress protein from Lactobacillus plantarum, in Escherichia coli.
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Appl Environ Microbiol,
75,
5273-5283.
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Y.Y.Tseng,
J.Dundas,
and
J.Liang
(2009).
Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns.
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J Mol Biol,
387,
451-464.
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F.E.Jenney,
and
M.W.Adams
(2008).
The impact of extremophiles on structural genomics (and vice versa).
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Extremophiles,
12,
39-50.
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I.M.Overton,
G.Padovani,
M.A.Girolami,
and
G.J.Barton
(2008).
ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction.
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Bioinformatics,
24,
901-907.
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K.L.Chao,
K.Lim,
C.Lehmann,
V.Doseeva,
A.J.Howard,
F.P.Schwarz,
and
O.Herzberg
(2008).
The Escherichia coli YdcF binds S-adenosyl-L-methionine and adopts an alpha/beta-fold characteristic of nucleotide-utilizing enzymes.
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Proteins,
72,
506-509.
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PDB code:
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M.E.Jurca,
S.Bottka,
and
A.Fehér
(2008).
Characterization of a family of Arabidopsis receptor-like cytoplasmic kinases (RLCK class VI).
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Plant Cell Rep,
27,
739-748.
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M.Lenman,
C.Sörensson,
and
E.Andreasson
(2008).
Enrichment of phosphoproteins and phosphopeptide derivatization identify universal stress proteins in elicitor-treated Arabidopsis.
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Mol Plant Microbe Interact,
21,
1275-1284.
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D.H.Shin,
J.Hou,
J.M.Chandonia,
D.Das,
I.G.Choi,
R.Kim,
and
S.H.Kim
(2007).
Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center.
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J Struct Funct Genomics,
8,
99.
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D.J.Murphy,
and
J.R.Brown
(2007).
Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.
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BMC Infect Dis,
7,
84.
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G.Scott,
and
C.R.Shyu
(2007).
Knowledge-driven multidimensional indexing structure for biomedical media database retrieval.
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IEEE Trans Inf Technol Biomed,
11,
320-331.
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S.K.Ruan,
K.H.Chin,
H.L.Shr,
P.C.Lyu,
A.H.Wang,
and
S.H.Chou
(2007).
Preliminary X-ray analysis of XC5848, a hypothetical ORFan protein with an Sm-like motif from Xanthomonas campestris.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
30-33.
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S.R.Sagurthi,
R.R.Panigrahi,
G.Gowda,
H.S.Savithri,
and
M.R.Murthy
(2007).
Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of universal stress protein F (YnaF) from Salmonella typhimurium.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
63,
957-960.
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S.S.Negi,
and
W.Braun
(2007).
Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces.
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J Mol Model,
13,
1157-1167.
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T.C.Terwilliger,
P.D.Adams,
N.W.Moriarty,
and
J.D.Cohn
(2007).
Ligand identification using electron-density map correlations.
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Acta Crystallogr D Biol Crystallogr,
63,
101-107.
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J.M.Chandonia,
S.H.Kim,
and
S.E.Brenner
(2006).
Target selection and deselection at the Berkeley Structural Genomics Center.
|
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Proteins,
62,
356-370.
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M.K.Ashby,
and
J.Houmard
(2006).
Cyanobacterial two-component proteins: structure, diversity, distribution, and evolution.
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Microbiol Mol Biol Rev,
70,
472-509.
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P.H.Chi,
C.R.Shyu,
and
D.Xu
(2006).
A fast SCOP fold classification system using content-based E-Predict algorithm.
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BMC Bioinformatics,
7,
362.
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S.Sivashankari,
and
P.Shanmughavel
(2006).
Functional annotation of hypothetical proteins - A review.
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Bioinformation,
1,
335-338.
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V.L.Arcus,
J.S.Lott,
J.M.Johnston,
and
E.N.Baker
(2006).
The potential impact of structural genomics on tuberculosis drug discovery.
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Drug Discov Today,
11,
28-34.
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W.Gao,
Y.Liu,
C.S.Giometti,
S.L.Tollaksen,
T.Khare,
L.Wu,
D.M.Klingeman,
M.W.Fields,
and
J.Zhou
(2006).
Knock-out of SO1377 gene, which encodes the member of a conserved hypothetical bacterial protein family COG2268, results in alteration of iron metabolism, increased spontaneous mutation and hydrogen peroxide sensitivity in Shewanella oneidensis MR-1.
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BMC Genomics,
7,
76.
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Y.Qiu,
V.Tereshko,
Y.Kim,
R.Zhang,
F.Collart,
M.Yousef,
A.Kossiakoff,
and
A.Joachimiak
(2006).
The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold.
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Proteins,
62,
8.
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PDB code:
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C.R.Guzzo,
R.A.Nagem,
L.M.Galvão-Botton,
B.G.Guimarães,
F.J.Medrano,
J.A.Barbosa,
and
C.S.Farah
(2005).
Expression, purification, crystallization and preliminary X-ray analysis of YaeQ (XAC2396) from Xanthomonas axonopodis pv. citri.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
493-495.
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C.Z.Zhou,
P.Meyer,
S.Quevillon-Cheruel,
I.L.De La Sierra-Gallay,
B.Collinet,
M.Graille,
K.Blondeau,
J.M.François,
N.Leulliot,
I.Sorel,
A.Poupon,
J.Janin,
and
H.Van Tilbeurgh
(2005).
Crystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new sequence family of the jelly-roll fold.
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Protein Sci,
14,
209-215.
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PDB codes:
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D.A.Siegele
(2005).
Universal stress proteins in Escherichia coli.
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J Bacteriol,
187,
6253-6254.
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E.Kuznetsova,
M.Proudfoot,
S.A.Sanders,
J.Reinking,
A.Savchenko,
C.H.Arrowsmith,
A.M.Edwards,
and
A.F.Yakunin
(2005).
Enzyme genomics: Application of general enzymatic screens to discover new enzymes.
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FEMS Microbiol Rev,
29,
263-279.
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I.Kifer,
O.Sasson,
and
M.Linial
(2005).
Predicting fold novelty based on ProtoNet hierarchical classification.
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Bioinformatics,
21,
1020-1027.
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K.H.Chin,
W.T.Kuo,
C.C.Chou,
H.L.Shr,
P.C.Lyu,
A.H.Wang,
and
S.H.Chou
(2005).
Cloning, purification, crystallization and preliminary X-ray analysis of XC229, a conserved hypothetical protein from Xanthomonas campestris.
|
| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
694-696.
|
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K.H.Chin,
Z.W.Huang,
K.C.Wei,
C.C.Chou,
C.C.Lee,
H.L.Shr,
F.P.Gao,
P.C.Lyu,
A.H.Wang,
and
S.H.Chou
(2005).
Preparation, crystallization and preliminary X-ray characterization of a conserved hypothetical protein XC1692 from Xanthomonas campestris.
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| |
Acta Crystallogr Sect F Struct Biol Cryst Commun,
61,
691-693.
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L.Nachin,
U.Nannmark,
and
T.Nyström
(2005).
Differential roles of the universal stress proteins of Escherichia coli in oxidative stress resistance, adhesion, and motility.
|
| |
J Bacteriol,
187,
6265-6272.
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M.Hamady,
T.H.Cheung,
K.Resing,
K.J.Cios,
and
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(2005).
Key challenges in proteomics and proteoinformatics. Progress in proteins.
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IEEE Eng Med Biol Mag,
24,
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M.P.Robertson,
H.Igel,
R.Baertsch,
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M.Ares,
and
W.G.Scott
(2005).
The structure of a rigorously conserved RNA element within the SARS virus genome.
|
| |
PLoS Biol,
3,
e5.
|
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PDB code:
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S.Quevillon-Cheruel,
N.Leulliot,
M.Graille,
N.Hervouet,
F.Coste,
H.Bénédetti,
C.Zelwer,
J.Janin,
and
H.Van Tilbeurgh
(2005).
Crystal structure of yeast YHR049W/FSH1, a member of the serine hydrolase family.
|
| |
Protein Sci,
14,
1350-1356.
|
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PDB code:
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|
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A.F.Yakunin,
A.A.Yee,
A.Savchenko,
A.M.Edwards,
and
C.H.Arrowsmith
(2004).
Structural proteomics: a tool for genome annotation.
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Curr Opin Chem Biol,
8,
42-48.
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A.Riboldi-Tunnicliffe,
C.J.Bent,
N.W.Isaacs,
and
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(2004).
Expression, purification and X-ray characterization of residues 18-230 from the pneumococcal histidine triad protein A (PhtA) from Streptococcus pneumoniae.
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Acta Crystallogr D Biol Crystallogr,
60,
926-928.
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I.L.de La Sierra-Gallay,
B.Collinet,
M.Graille,
S.Quevillon-Cheruel,
D.Liger,
P.Minard,
K.Blondeau,
G.Henckes,
R.Aufrère,
N.Leulliot,
C.Z.Zhou,
I.Sorel,
J.L.Ferrer,
A.Poupon,
J.Janin,
and
H.van Tilbeurgh
(2004).
Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: close structural resemblance to E. coli pantothenate kinase.
|
| |
Proteins,
54,
776-783.
|
|
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PDB code:
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J.Skolnick,
D.Kihara,
and
Y.Zhang
(2004).
Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm.
|
| |
Proteins,
56,
502-518.
|
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M.Y.Galperin,
and
E.V.Koonin
(2004).
'Conserved hypothetical' proteins: prioritization of targets for experimental study.
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| |
Nucleic Acids Res,
32,
5452-5463.
|
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A.Matte,
J.Sivaraman,
I.Ekiel,
K.Gehring,
Z.Jia,
and
M.Cygler
(2003).
Contribution of structural genomics to understanding the biology of Escherichia coli.
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J Bacteriol,
185,
3994-4002.
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C.Zhang,
and
S.H.Kim
(2003).
Overview of structural genomics: from structure to function.
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| |
Curr Opin Chem Biol,
7,
28-32.
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D.Frishman
(2003).
What we have learned about prokaryotes from structural genomics.
|
| |
OMICS,
7,
211-224.
|
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|
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K.Kvint,
L.Nachin,
A.Diez,
and
T.Nyström
(2003).
The bacterial universal stress protein: function and regulation.
|
| |
Curr Opin Microbiol,
6,
140-145.
|
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K.S.Makarova,
and
E.V.Koonin
(2003).
Comparative genomics of Archaea: how much have we learned in six years, and what's next?
|
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Genome Biol,
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PDB code:
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PDB code:
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PDB code:
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PDB codes:
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When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families.
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PDB code:
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PDB code:
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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.
|
|
Links
