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PDBsum entry 1gh9
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Structural genomics, unknown function
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PDB id
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1gh9
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DOI no:
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Nat Struct Biol
7:903-909
(2000)
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PubMed id:
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Structural proteomics of an archaeon.
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D.Christendat,
A.Yee,
A.Dharamsi,
Y.Kluger,
A.Savchenko,
J.R.Cort,
V.Booth,
C.D.Mackereth,
V.Saridakis,
I.Ekiel,
G.Kozlov,
K.L.Maxwell,
N.Wu,
L.P.McIntosh,
K.Gehring,
M.A.Kennedy,
A.R.Davidson,
E.F.Pai,
M.Gerstein,
A.M.Edwards,
C.H.Arrowsmith.
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ABSTRACT
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A set of 424 nonmembrane proteins from Methanobacterium thermoautotrophicum were
cloned, expressed and purified for structural studies. Of these, approximately
20% were found to be suitable candidates for X-ray crystallographic or NMR
spectroscopic analysis without further optimization of conditions, providing an
estimate of the number of the most accessible structural targets in the
proteome. A retrospective analysis of the experimental behavior of these
proteins suggested some simple relations between sequence and solubility,
implying that data bases of protein properties will be useful in optimizing high
throughput strategies. Of the first 10 structures determined, several provided
clues to biochemical functions that were not detectable from sequence analysis,
and in many cases these putative functions could be readily confirmed by
biochemical methods. This demonstrates that structural proteomics is feasible
and can play a central role in functional genomics.
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Selected figure(s)
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Figure 1.
Figure 1. M.th. target ORFs. A histogram representing the
numbers of different classes of M.th. ORFs according to
predicted protein size showing unbiased sampling of nonmembrane
proteins of unknown structure.
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Figure 4.
Figure 4. Backbone ribbon representations of the first 10
protein structures.  -sheets
are shown in cyan and  -helices
in red. Bound cofactors and ligands are shown as ball-and-stick
models and metal ions as spheres. The M.th. gene number is given
along with the confirmed and/or putative (asterisks) biochemical
function of the protein. †Note that MTH150 is a homohexamer,
and MTH152 and MTH129 are homodimers, although only a single
subunit is displayed here.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2000,
7,
903-909)
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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A.Lemak,
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J Biomol NMR,
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K.Prymula,
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"Fuzzy oil drop" model applied to individual small proteins built of 70 amino acids.
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J Mol Model,
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M.Vedadi,
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Biophysical characterization of recombinant proteins: a key to higher structural genomics success.
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J Struct Biol,
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P.Zhou,
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J Biomol NMR,
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C.N.Magnan,
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SOLpro: accurate sequence-based prediction of protein solubility.
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Bioinformatics,
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Pharm Res,
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J Struct Funct Genomics,
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G.A.Senisterra,
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High throughput methods of assessing protein stability and aggregation.
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Mol Biosyst,
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K.Kwon,
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M.P.Williamson,
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J Biomol NMR,
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Chembiochem,
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A.J.Martin-Galiano,
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Predicting experimental properties of integral membrane proteins by a naive Bayes approach.
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Proteins,
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F.E.Jenney,
and
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The impact of extremophiles on structural genomics (and vice versa).
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Extremophiles,
12,
39-50.
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L.C.Ngoka
(2008).
Sample prep for proteomics of breast cancer: proteomics and gene ontology reveal dramatic differences in protein solubilization preferences of radioimmunoprecipitation assay and urea lysis buffers.
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Proteome Sci,
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30.
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A.Kato,
K.Maki,
T.Ebina,
K.Kuwajima,
K.Soda,
and
Y.Kuroda
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Mutational analysis of protein solubility enhancement using short peptide tags.
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Biopolymers,
85,
12-18.
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A.Korepanova,
J.D.Moore,
H.B.Nguyen,
Y.Hua,
T.A.Cross,
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Expression of membrane proteins from Mycobacterium tuberculosis in Escherichia coli as fusions with maltose binding protein.
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Protein Expr Purif,
53,
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A.Schlessinger,
J.Liu,
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Natively Unstructured Loops Differ from Other Loops.
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PLoS Comput Biol,
3,
e140.
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B.K.Koo,
J.Jung,
H.Jung,
H.W.Nam,
Y.S.Kim,
A.Yee,
and
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Solution structure of the hypothetical novel-fold protein TA0956 from Thermoplasma acidophilum.
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Proteins,
69,
444-447.
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PDB code:
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E.Williams,
T.M.Lowe,
J.Savas,
and
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Microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus exposed to gamma irradiation.
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Extremophiles,
11,
19-29.
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F.K.Pettit,
E.Bare,
A.Tsai,
and
J.U.Bowie
(2007).
HotPatch: a statistical approach to finding biologically relevant features on protein surfaces.
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J Mol Biol,
369,
863-879.
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F.L.Moseley,
K.A.Bicknell,
M.S.Marber,
and
G.Brooks
(2007).
The use of proteomics to identify novel therapeutic targets for the treatment of disease.
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J Pharm Pharmacol,
59,
609-628.
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H.Iwaki,
T.Muraki,
S.Ishihara,
Y.Hasegawa,
K.N.Rankin,
T.Sulea,
J.Boyd,
and
P.C.Lau
(2007).
Characterization of a pseudomonad 2-nitrobenzoate nitroreductase and its catabolic pathway-associated 2-hydroxylaminobenzoate mutase and a chemoreceptor involved in 2-nitrobenzoate chemotaxis.
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J Bacteriol,
189,
3502-3514.
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L.Slabinski,
L.Jaroszewski,
A.P.Rodrigues,
L.Rychlewski,
I.A.Wilson,
S.A.Lesley,
and
A.Godzik
(2007).
The challenge of protein structure determination--lessons from structural genomics.
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Protein Sci,
16,
2472-2482.
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M.A.White,
K.M.Clark,
E.J.Grayhack,
and
M.E.Dumont
(2007).
Characteristics affecting expression and solubilization of yeast membrane proteins.
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J Mol Biol,
365,
621-636.
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M.Forstner,
L.Leder,
and
L.M.Mayr
(2007).
Optimization of protein expression systems for modern drug discovery.
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Expert Rev Proteomics,
4,
67-78.
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M.P.Cusack,
B.Thibert,
D.E.Bredesen,
and
G.Del Rio
(2007).
Efficient identification of critical residues based only on protein structure by network analysis.
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PLoS ONE,
2,
e421.
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N.Mirkovic,
Z.Li,
A.Parnassa,
and
D.Murray
(2007).
Strategies for high-throughput comparative modeling: applications to leverage analysis in structural genomics and protein family organization.
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Proteins,
66,
766-777.
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N.R.Zaccai,
K.Yunus,
S.M.Matthews,
A.C.Fisher,
and
R.J.Falconer
(2007).
Refolding of a membrane protein in a microfluidics reactor.
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Eur Biophys J,
36,
581-588.
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P.Smialowski,
A.J.Martin-Galiano,
A.Mikolajka,
T.Girschick,
T.A.Holak,
and
D.Frishman
(2007).
Protein solubility: sequence based prediction and experimental verification.
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Bioinformatics,
23,
2536-2542.
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S.R.Trevino,
J.M.Scholtz,
and
C.N.Pace
(2007).
Amino acid contribution to protein solubility: Asp, Glu, and Ser contribute more favorably than the other hydrophilic amino acids in RNase Sa.
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J Mol Biol,
366,
449-460.
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Y.N.Kang,
A.Tran,
R.H.White,
and
S.E.Ealick
(2007).
A novel function for the N-terminal nucleophile hydrolase fold demonstrated by the structure of an archaeal inosine monophosphate cyclohydrolase.
|
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Biochemistry,
46,
5050-5062.
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PDB codes:
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B.R.Jefferys,
L.A.Kelley,
M.J.Sergot,
J.Fox,
and
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(2006).
Capturing expert knowledge with argumentation: a case study in bioinformatics.
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Bioinformatics,
22,
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M.Hammarström,
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N.Hellgren,
T.Härd,
and
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(2006).
Effect of N-terminal solubility enhancing fusion proteins on yield of purified target protein.
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J Struct Funct Genomics,
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M.Vedadi,
F.H.Niesen,
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O.Y.Fedorov,
P.J.Finerty,
G.A.Wasney,
R.Yeung,
C.Arrowsmith,
L.J.Ball,
H.Berglund,
R.Hui,
B.D.Marsden,
P.Nordlund,
M.Sundstrom,
J.Weigelt,
and
A.M.Edwards
(2006).
Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination.
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Proc Natl Acad Sci U S A,
103,
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N.P.Cowieson,
B.Wensley,
P.Listwan,
D.A.Hume,
B.Kobe,
and
J.L.Martin
(2006).
An automatable screen for the rapid identification of proteins amenable to refolding.
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Proteomics,
6,
1750-1757.
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P.M.Alzari,
H.Berglund,
N.S.Berrow,
E.Blagova,
D.Busso,
C.Cambillau,
V.Campanacci,
E.Christodoulou,
S.Eiler,
M.J.Fogg,
G.Folkers,
A.Geerlof,
D.Hart,
A.Haouz,
M.D.Herman,
S.Macieira,
P.Nordlund,
A.Perrakis,
S.Quevillon-Cheruel,
F.Tarandeau,
H.van Tilbeurgh,
T.Unger,
M.P.Luna-Vargas,
M.Velarde,
M.Willmanns,
and
R.J.Owens
(2006).
Implementation of semi-automated cloning and prokaryotic expression screening: the impact of SPINE.
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Acta Crystallogr D Biol Crystallogr,
62,
1103-1113.
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P.Smialowski,
T.Schmidt,
J.Cox,
A.Kirschner,
and
D.Frishman
(2006).
Will my protein crystallize? A sequence-based predictor.
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Proteins,
62,
343-355.
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S.Surade,
M.Klein,
P.C.Stolt-Bergner,
C.Muenke,
A.Roy,
and
H.Michel
(2006).
Comparative analysis and "expression space" coverage of the production of prokaryotic membrane proteins for structural genomics.
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Protein Sci,
15,
2178-2189.
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A.Korepanova,
F.P.Gao,
Y.Hua,
H.Qin,
R.K.Nakamoto,
and
T.A.Cross
(2005).
Cloning and expression of multiple integral membrane proteins from Mycobacterium tuberculosis in Escherichia coli.
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Protein Sci,
14,
148-158.
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E.Dobrovetsky,
M.L.Lu,
R.Andorn-Broza,
G.Khutoreskaya,
J.E.Bray,
A.Savchenko,
C.H.Arrowsmith,
A.M.Edwards,
and
C.M.Koth
(2005).
High-throughput production of prokaryotic membrane proteins.
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J Struct Funct Genomics,
6,
33-50.
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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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H.L.Liu,
and
J.P.Hsu
(2005).
Recent developments in structural proteomics for protein structure determination.
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Proteomics,
5,
2056-2068.
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J.Eichler,
and
M.W.Adams
(2005).
Posttranslational protein modification in Archaea.
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Microbiol Mol Biol Rev,
69,
393-425.
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K.S.Makarova,
and
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(2005).
Evolutionary and functional genomics of the Archaea.
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Curr Opin Microbiol,
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M.Neerathilingam,
L.H.Greene,
S.A.Colebrooke,
I.D.Campbell,
and
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(2005).
Quantitation of protein expression in a cell-free system: Efficient detection of yields and 19F NMR to identify folded protein.
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J Biomol NMR,
31,
11-19.
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R.Page,
W.Peti,
I.A.Wilson,
R.C.Stevens,
and
K.Wüthrich
(2005).
NMR screening and crystal quality of bacterially expressed prokaryotic and eukaryotic proteins in a structural genomics pipeline.
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Proc Natl Acad Sci U S A,
102,
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S.Züger,
and
H.Iwai
(2005).
Intein-based biosynthetic incorporation of unlabeled protein tags into isotopically labeled proteins for NMR studies.
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Nat Biotechnol,
23,
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T.Luan,
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and
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(2005).
Optimization of resolution and sensitivity of 4D NOESY using multi-dimensional decomposition.
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J Biomol NMR,
33,
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U.Korf,
T.Kohl,
H.van der Zandt,
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M.Schnölzer,
H.Ottleben,
S.Wiemann,
and
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(2005).
Large-scale protein expression for proteome research.
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Proteomics,
5,
3571-3580.
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W.Peti,
R.Page,
K.Moy,
M.O'Neil-Johnson,
I.A.Wilson,
R.C.Stevens,
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K.Wüthrich
(2005).
Towards miniaturization of a structural genomics pipeline using micro-expression and microcoil NMR.
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J Struct Funct Genomics,
6,
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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
T.J.Mitchell
(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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C.H.Lee,
J.W.Jung,
A.Yee,
C.H.Arrowsmith,
and
W.Lee
(2004).
Solution structure of a novel calcium binding protein, MTH1880, from Methanobacterium thermoautotrophicum.
|
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Protein Sci,
13,
1148-1154.
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PDB codes:
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C.H.Luan,
S.Qiu,
J.B.Finley,
M.Carson,
R.J.Gray,
W.Huang,
D.Johnson,
J.Tsao,
J.Reboul,
P.Vaglio,
D.E.Hill,
M.Vidal,
L.J.Delucas,
and
M.Luo
(2004).
High-throughput expression of C. elegans proteins.
|
| |
Genome Res,
14,
2102-2110.
|
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C.Herve du Penhoat,
H.S.Atreya,
Y.Shen,
G.Liu,
T.B.Acton,
R.Xiao,
Z.Li,
D.Murray,
G.T.Montelione,
and
T.Szyperski
(2004).
The NMR solution structure of the 30S ribosomal protein S27e encoded in gene RS27_ARCFU of Archaeoglobus fulgidis reveals a novel protein fold.
|
| |
Protein Sci,
13,
1407-1416.
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PDB code:
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F.J.Blanco,
A.Yee,
R.Campos-Olivas,
A.R.Ortiz,
D.Devos,
A.Valencia,
C.H.Arrowsmith,
and
M.Rico
(2004).
Solution structure of the hypothetical protein Mth677 from Methanobacterium thermoautotrophicum: a novel alpha+beta fold.
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| |
Protein Sci,
13,
1458-1465.
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PDB code:
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F.Pazos,
and
M.J.Sternberg
(2004).
Automated prediction of protein function and detection of functional sites from structure.
|
| |
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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
