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PDBsum entry 1jw2
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Gene regulation
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PDB id
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1jw2
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Contents |
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* Residue conservation analysis
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DOI no:
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Proc Natl Acad Sci U S A
99:1825-1830
(2002)
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PubMed id:
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An NMR approach to structural proteomics.
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A.Yee,
X.Chang,
A.Pineda-Lucena,
B.Wu,
A.Semesi,
B.Le,
T.Ramelot,
G.M.Lee,
S.Bhattacharyya,
P.Gutierrez,
A.Denisov,
C.H.Lee,
J.R.Cort,
G.Kozlov,
J.Liao,
G.Finak,
L.Chen,
D.Wishart,
W.Lee,
L.P.McIntosh,
K.Gehring,
M.A.Kennedy,
A.M.Edwards,
C.H.Arrowsmith.
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ABSTRACT
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The influx of genomic sequence information has led to the concept of structural
proteomics, the determination of protein structures on a genome-wide scale. Here
we describe an approach to structural proteomics of small proteins using NMR
spectroscopy. Over 500 small proteins from several organisms were cloned,
expressed, purified, and evaluated by NMR. Although there was variability among
proteomes, overall 20% of these proteins were found to be readily amenable to
NMR structure determination. NMR sample preparation was centralized in one
facility, and a distributive approach was used for NMR data collection and
analysis. Twelve structures are reported here as part of this approach, which
allowed us to infer putative functions for several conserved hypothetical
proteins.
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Selected figure(s)
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Figure 1.
Fig. 1. Histogram of the number of proteins cloned
(blue), expressed (red), and soluble (gray) from each organism.
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Figure 3.
Fig. 3. 15N HSQC spectra and the backbone ribbon
representations of the 12 structures presented in this paper.
All HSQCs are plotted from 6.0-10.5 ppm in the 1H dimension (x
axis) and from 107 to 133 ppm in the 15N dimension (y axis). The
number of residues for each protein is indicated on the HSQC
spectrum.  -sheets are
shown in cyan, and  -helices
are shown in red. N-terminal residues 1-20 of yedF_ecoli and
Myxv156r are unstructured and not shown. C-terminal residues
198-208 of Mth1692 are unstructured and not shown. All structure
diagrams were created by using the MOLAUTO program within
MOLSCRIPT (17).
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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,
A.Gutmanas,
S.Chitayat,
M.Karra,
C.Farès,
M.Sunnerhagen,
and
C.H.Arrowsmith
(2011).
A novel strategy for NMR resonance assignment and protein structure determination.
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J Biomol NMR,
49,
27-38.
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D.K.Tay,
G.Rajagopalan,
X.Li,
Y.Chen,
L.H.Lua,
and
S.S.Leong
(2011).
A new bioproduction route for a novel antimicrobial peptide.
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Biotechnol Bioeng,
108,
572-581.
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G.A.Bermejo,
and
M.Llinás
(2010).
Structure-oriented methods for protein NMR data analysis.
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Prog Nucl Magn Reson Spectrosc,
56,
311-328.
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K.Prymula,
K.Sałapa,
and
I.Roterman
(2010).
"Fuzzy oil drop" model applied to individual small proteins built of 70 amino acids.
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J Mol Model,
16,
1269-1282.
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B.Bardiaux,
A.Bernard,
W.Rieping,
M.Habeck,
T.E.Malliavin,
and
M.Nilges
(2009).
Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA.
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Proteins,
75,
569-585.
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H.Arai,
S.Watanabe,
T.Kigawa,
and
M.Yamamura
(2009).
A new modeling method in feature construction for the HSQC spectra screening problem.
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Bioinformatics,
25,
948-953.
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M.P.Williamson,
and
C.J.Craven
(2009).
Automated protein structure calculation from NMR data.
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J Biomol NMR,
43,
131-143.
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M.Swain,
and
H.S.Atreya
(2009).
CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts.
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J Biomol NMR,
44,
185-194.
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R.M.Rasia,
M.Noirclerc-Savoye,
N.G.Bologna,
B.Gallet,
M.J.Plevin,
L.Blanchard,
J.F.Palatnik,
B.Brutscher,
T.Vernet,
and
J.Boisbouvier
(2009).
Parallel screening and optimization of protein constructs for structural studies.
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Protein Sci,
18,
434-439.
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A.Lemak,
C.A.Steren,
C.H.Arrowsmith,
and
M.Llinás
(2008).
Sequence specific resonance assignment via Multicanonical Monte Carlo search using an ABACUS approach.
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J Biomol NMR,
41,
29-41.
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B.J.Wylie,
L.J.Sperling,
and
C.M.Rienstra
(2008).
Isotropic chemical shifts in magic-angle spinning NMR spectra of proteins.
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Phys Chem Chem Phys,
10,
405-413.
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B.Wu,
A.Yee,
Y.J.Huang,
T.A.Ramelot,
J.R.Cort,
A.Semesi,
J.W.Jung,
W.Lee,
G.T.Montelione,
M.A.Kennedy,
and
C.H.Arrowsmith
(2008).
The solution structure of ribosomal protein S17E from Methanobacterium thermoautotrophicum: a structural homolog of the FF domain.
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Protein Sci,
17,
583-588.
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PDB code:
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B.Wu,
J.Lukin,
A.Yee,
A.Lemak,
A.Semesi,
T.A.Ramelot,
M.A.Kennedy,
and
C.H.Arrowsmith
(2008).
Solution structure of ribosomal protein L40E, a unique C4 zinc finger protein encoded by archaeon Sulfolobus solfataricus.
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Protein Sci,
17,
589-596.
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PDB code:
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H.P.Narra,
M.H.Cordes,
and
H.Ochman
(2008).
Structural features and the persistence of acquired proteins.
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Proteomics,
8,
4772-4781.
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J.J.Kuszewski,
R.A.Thottungal,
G.M.Clore,
and
C.D.Schwieters
(2008).
Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm.
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J Biomol NMR,
41,
221-239.
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J.Shin,
W.Lee,
and
W.Lee
(2008).
Structural proteomics by NMR spectroscopy.
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Expert Rev Proteomics,
5,
589-601.
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M.Billeter,
G.Wagner,
and
K.Wüthrich
(2008).
Solution NMR structure determination of proteins revisited.
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J Biomol NMR,
42,
155-158.
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A.Kato,
K.Maki,
T.Ebina,
K.Kuwajima,
K.Soda,
and
Y.Kuroda
(2007).
Mutational analysis of protein solubility enhancement using short peptide tags.
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Biopolymers,
85,
12-18.
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C.Madrid,
C.Balsalobre,
J.García,
and
A.Juárez
(2007).
The novel Hha/YmoA family of nucleoid-associated proteins: use of structural mimicry to modulate the activity of the H-NS family of proteins.
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Mol Microbiol,
63,
7.
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J.Lee,
R.Page,
R.García-Contreras,
J.M.Palermino,
X.S.Zhang,
O.Doshi,
T.K.Wood,
and
W.Peti
(2007).
Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance.
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J Mol Biol,
373,
11-26.
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PDB code:
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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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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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D.Staunton,
R.Schlinkert,
G.Zanetti,
S.A.Colebrook,
and
I.D.Campbell
(2006).
Cell-free expression and selective isotope labelling in protein NMR.
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Magn Reson Chem,
44,
S2-S9.
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K.G.Valentine,
M.S.Pometun,
J.M.Kielec,
R.E.Baigelman,
J.K.Staub,
K.L.Owens,
and
A.J.Wand
(2006).
Magnetic susceptibility-induced alignment of proteins in reverse micelles.
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J Am Chem Soc,
128,
15930-15931.
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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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T.Ducat,
N.Declerck,
T.Gostan,
M.Kochoyan,
and
H.Déméné
(2006).
Rapid determination of protein solubility and stability conditions for NMR studies using incomplete factorial design.
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J Biomol NMR,
34,
137-151.
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T.Etezady-Esfarjani,
T.Herrmann,
R.Horst,
and
K.Wüthrich
(2006).
Automated protein NMR structure determination in crude cell-extract.
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J Biomol NMR,
34,
3.
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T.Hondoh,
A.Kato,
S.Yokoyama,
and
Y.Kuroda
(2006).
Computer-aided NMR assay for detecting natively folded structural domains.
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Protein Sci,
15,
871-883.
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Y.C.Lin,
G.Liu,
Y.Shen,
C.Bertonati,
A.Yee,
B.Honig,
C.H.Arrowsmith,
and
T.Szyperski
(2006).
NMR structure of protein PA2021 from Pseudomonas aeruginosa.
|
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Proteins,
65,
767-770.
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A.Grishaev,
C.A.Steren,
B.Wu,
A.Pineda-Lucena,
C.Arrowsmith,
and
M.Llinás
(2005).
ABACUS, a direct method for protein NMR structure computation via assembly of fragments.
|
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Proteins,
61,
36-43.
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A.Kalia,
and
R.P.Gupta
(2005).
Proteomics: a paradigm shift.
|
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Crit Rev Biotechnol,
25,
173-198.
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C.H.Penhoat,
Z.Li,
H.S.Atreya,
S.Kim,
A.Yee,
R.Xiao,
D.Murray,
C.H.Arrowsmith,
and
T.Szyperski
(2005).
NMR solution structure of Thermotoga maritima protein TM1509 reveals a Zn-metalloprotease-like tertiary structure.
|
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J Struct Funct Genomics,
6,
51-62.
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PDB code:
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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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G.Liu,
Y.Shen,
H.S.Atreya,
D.Parish,
Y.Shao,
D.K.Sukumaran,
R.Xiao,
A.Yee,
A.Lemak,
A.Bhattacharya,
T.A.Acton,
C.H.Arrowsmith,
G.T.Montelione,
and
T.Szyperski
(2005).
NMR data collection and analysis protocol for high-throughput protein structure determination.
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Proc Natl Acad Sci U S A,
102,
10487-10492.
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PDB codes:
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J.A.Gaspar,
C.Liu,
K.A.Vassall,
G.Meglei,
R.Stephen,
P.B.Stathopulos,
A.Pineda-Lucena,
B.Wu,
A.Yee,
C.H.Arrowsmith,
and
E.M.Meiering
(2005).
A novel member of the YchN-like fold: solution structure of the hypothetical protein Tm0979 from Thermotoga maritima.
|
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Protein Sci,
14,
216-223.
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PDB code:
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M.Neerathilingam,
L.H.Greene,
S.A.Colebrooke,
I.D.Campbell,
and
D.Staunton
(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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M.S.Willis,
J.K.Hogan,
P.Prabhakar,
X.Liu,
K.Tsai,
Y.Wei,
and
T.Fox
(2005).
Investigation of protein refolding using a fractional factorial screen: a study of reagent effects and interactions.
|
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Protein Sci,
14,
1818-1826.
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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,
1901-1905.
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S.Málková,
F.Long,
R.V.Stahelin,
S.V.Pingali,
D.Murray,
W.Cho,
and
M.L.Schlossman
(2005).
X-ray reflectivity studies of cPLA2{alpha}-C2 domains adsorbed onto Langmuir monolayers of SOPC.
|
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Biophys J,
89,
1861-1873.
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S.Rodríguez,
J.M.Nieto,
C.Madrid,
and
A.Juárez
(2005).
Functional replacement of the oligomerization domain of H-NS by the Hha protein of Escherichia coli.
|
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J Bacteriol,
187,
5452-5459.
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W.Peti,
R.Page,
K.Moy,
M.O'Neil-Johnson,
I.A.Wilson,
R.C.Stevens,
and
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,
259-267.
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|
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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.
|
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Protein Sci,
13,
1407-1416.
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PDB code:
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D.McMullan,
R.Schwarzenbacher,
L.Jaroszewski,
F.von Delft,
H.E.Klock,
J.Vincent,
K.Quijano,
P.Abdubek,
E.Ambing,
T.Biorac,
L.S.Brinen,
J.M.Canaves,
X.Dai,
A.M.Deacon,
M.DiDonato,
M.A.Elsliger,
S.Eshaghi,
R.Floyd,
A.Godzik,
C.Grittini,
S.K.Grzechnik,
E.Hampton,
C.Karlak,
E.Koesema,
A.Kreusch,
P.Kuhn,
I.Levin,
T.M.McPhillips,
M.D.Miller,
A.Morse,
K.Moy,
J.Ouyang,
R.Page,
R.Reyes,
F.Rezezadeh,
A.Robb,
E.Sims,
G.Spraggon,
R.C.Stevens,
H.van den Bedem,
J.Velasquez,
X.Wang,
B.West,
G.Wolf,
Q.Xu,
K.O.Hodgson,
J.Wooley,
S.A.Lesley,
and
I.A.Wilson
(2004).
Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution.
|
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Proteins,
56,
615-618.
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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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J.M.Canaves
(2004).
Predicted role for the archease protein family based on structural and sequence analysis of TM1083 and MTH1598, two proteins structurally characterized through structural genomics efforts.
|
| |
Proteins,
56,
19-27.
|
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K.Ozawa,
M.J.Headlam,
P.M.Schaeffer,
B.R.Henderson,
N.E.Dixon,
and
G.Otting
(2004).
Optimization of an Escherichia coli system for cell-free synthesis of selectively N-labelled proteins for rapid analysis by NMR spectroscopy.
|
| |
Eur J Biochem,
271,
4084-4093.
|
|
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P.B.Stathopulos,
G.A.Scholz,
Y.M.Hwang,
J.A.Rumfeldt,
J.R.Lepock,
and
E.M.Meiering
(2004).
Sonication of proteins causes formation of aggregates that resemble amyloid.
|
| |
Protein Sci,
13,
3017-3027.
|
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V.Anantharaman,
and
L.Aravind
(2004).
The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies.
|
| |
Proteins,
56,
795-807.
|
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A.Sali,
R.Glaeser,
T.Earnest,
and
W.Baumeister
(2003).
From words to literature in structural proteomics.
|
| |
Nature,
422,
216-225.
|
|
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A.Savchenko,
A.Yee,
A.Khachatryan,
T.Skarina,
E.Evdokimova,
M.Pavlova,
A.Semesi,
J.Northey,
S.Beasley,
N.Lan,
R.Das,
M.Gerstein,
C.H.Arrowmith,
and
A.M.Edwards
(2003).
Strategies for structural proteomics of prokaryotes: Quantifying the advantages of studying orthologous proteins and of using both NMR and X-ray crystallography approaches.
|
| |
Proteins,
50,
392-399.
|
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A.Stark,
and
R.B.Russell
(2003).
Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.
|
| |
Nucleic Acids Res,
31,
3341-3344.
|
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B.Wu,
A.Yee,
A.Pineda-Lucena,
A.Semesi,
T.A.Ramelot,
J.R.Cort,
J.W.Jung,
A.Edwards,
W.Lee,
M.Kennedy,
and
C.H.Arrowsmith
(2003).
Solution structure of ribosomal protein S28E from Methanobacterium thermoautotrophicum.
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| |
Protein Sci,
12,
2831-2837.
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PDB code:
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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.
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OMICS,
7,
211-224.
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K.L.Maxwell,
D.Bona,
C.Liu,
C.H.Arrowsmith,
and
A.M.Edwards
(2003).
Refolding out of guanidine hydrochloride is an effective approach for high-throughput structural studies of small proteins.
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| |
Protein Sci,
12,
2073-2080.
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P.Braun,
and
J.LaBaer
(2003).
High throughput protein production for functional proteomics.
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| |
Trends Biotechnol,
21,
383-388.
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S.Yokoyama
(2003).
Protein expression systems for structural genomics and proteomics.
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| |
Curr Opin Chem Biol,
7,
39-43.
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T.A.Ramelot,
J.R.Cort,
A.A.Yee,
A.Semesi,
A.M.Edwards,
C.H.Arrowsmith,
and
M.A.Kennedy
(2002).
NMR structure of the Escherichia coli protein YacG: a novel sequence motif in the zinc-finger family of proteins.
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| |
Proteins,
49,
289-293.
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PDB code:
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V.Reinke,
and
K.P.White
(2002).
Developmental genomic approaches in model organisms.
|
| |
Annu Rev Genomics Hum Genet,
3,
153-178.
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|
,
(2002).
Current awareness on comparative and functional genomics.
|
| |
Comp Funct Genomics,
3,
389-396.
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F.Schafer,
A.Schafer,
and
K.Steinert
(2002).
A highly specific system for efficient enzymatic removal of tags from recombinant proteins.
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| |
J Biomol Tech,
13,
158-171.
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F.Schafer,
U.Romer,
M.Emmerlich,
J.Blumer,
H.Lubenow,
and
K.Steinert
(2002).
Automated high-throughput purification of 6xHis-tagged proteins.
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J Biomol Tech,
13,
131-142.
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M.B.Schmid
(2002).
Structural proteomics: the potential of high-throughput structure determination.
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| |
Trends Microbiol,
10,
S27-S31.
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S.F.Betz,
S.M.Baxter,
and
J.S.Fetrow
(2002).
Function first: a powerful approach to post-genomic drug discovery.
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Drug Discov Today,
7,
865-871.
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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
