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PDBsum entry 1vee
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Structural genomics, unknown function
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PDB id
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1vee
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Contents |
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* Residue conservation analysis
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PDB id:
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| Name: |
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Structural genomics, unknown function
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Title:
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Nmr structure of the hypothetical rhodanese domain at4g01050 from arabidopsis thaliana
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Structure:
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Proline-rich protein family. Chain: a. Fragment: rhodanese hypothetical domain. Synonym: hypothetical protein rafl06-68-j04. Engineered: yes
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Source:
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Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: riken cdna rafl06-68-j04. Other_details: e.Coli cell-free protein synthesis
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NMR struc:
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20 models
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Authors:
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D.Pantoja-Uceda,B.Lopez-Mendez,S.Koshiba,M.Inoue,T.Kigawa,T.Terada, M.Shirouzu,A.Tanaka,M.Seki,K.Shinozaki,S.Yokoyama,P.Guntert,Riken Structural Genomics/proteomics Initiative (Rsgi)
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Key ref:
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D.Pantoja-Uceda
et al.
(2005).
Solution structure of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana.
Protein Sci,
14,
224-230.
PubMed id:
DOI:
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Date:
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30-Mar-04
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Release date:
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25-Jan-05
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PROCHECK
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Headers
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References
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Q9M158
(STR4_ARATH) -
Rhodanese-like domain-containing protein 4, chloroplastic from Arabidopsis thaliana
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Seq:
Struc:
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466 a.a.
134 a.a.*
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Key: |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 12 residue positions (black
crosses)
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DOI no:
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Protein Sci
14:224-230
(2005)
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PubMed id:
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Solution structure of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana.
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D.Pantoja-Uceda,
B.López-Méndez,
S.Koshiba,
M.Inoue,
T.Kigawa,
T.Terada,
M.Shirouzu,
A.Tanaka,
M.Seki,
K.Shinozaki,
S.Yokoyama,
P.Güntert.
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ABSTRACT
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The three-dimensional structure of the rhodanese homology domain
At4g01050(175-195) from Arabidopsis thaliana has been determined by solution
nuclear magnetic resonance methods based on 3043 upper distance limits derived
from NOE intensities measured in three-dimensional NOESY spectra. The structure
shows a backbone root mean square deviation to the mean coordinates of 0.43 A
for the structured residues 7-125. The fold consists of a central parallel
beta-sheet with five strands in the order 1-5-4-2-3 and arranged in the
conventional counterclockwise twist, and helices packing against each side of
the beta-sheet. Comparison with the sequences of other proteins with a rhodanese
homology domain in Arabidopsis thaliana indicated residues that could play an
important role in the scaffold of the rhodanese homology domain. Finally, a
three-dimensional structure comparison of the present noncatalytic rhodanese
homology domain with the noncatalytic rhodanese domains of sulfurtransferases
from other organisms discloses differences in the length and conformation of
loops that could throw light on the role of the noncatalytic rhodanese domain in
sulfurtransferases.
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Selected figure(s)
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Figure 1.
Figure 1. Structure-based sequence alignment of the
rhodanese and rhodanese homology domains with known structure
according to the program DALI (Holm and Sander 1996). Domain
names are as in Table 2 Go- . The
catalytic position is shown in italics. Residues in helices or
 -strands are
highlighted in green and in cyan, respectively, and  -helices and
-strands are
labeled.
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The above figure is
reprinted
by permission from the Protein Society:
Protein Sci
(2005,
14,
224-230)
copyright 2005.
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Figure was
selected
by the author.
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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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J.Papenbrock,
S.Guretzki,
and
M.Henne
(2011).
Latest news about the sulfurtransferase protein family of higher plants.
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Amino Acids,
41,
43-57.
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D.Pantoja-Uceda,
J.L.Arolas,
F.X.Aviles,
J.Santoro,
S.Ventura,
and
C.P.Sommerhoff
(2009).
Deciphering the structural basis that guides the oxidative folding of leech-derived tryptase inhibitor.
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J Biol Chem,
284,
35612-35620.
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PDB codes:
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P.Güntert
(2009).
Automated structure determination from NMR spectra.
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Eur Biophys J,
38,
129-143.
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S.Jurić,
K.Hazler-Pilepić,
A.Tomasić,
H.Lepedus,
B.Jelicić,
S.Puthiyaveetil,
T.Bionda,
L.Vojta,
J.F.Allen,
E.Schleiff,
and
H.Fulgosi
(2009).
Tethering of ferredoxin:NADP+ oxidoreductase to thylakoid membranes is mediated by novel chloroplast protein TROL.
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Plant J,
60,
783-794.
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D.M.Standley,
H.Toh,
and
H.Nakamura
(2008).
Functional annotation by sequence-weighted structure alignments: statistical analysis and case studies from the Protein 3000 structural genomics project in Japan.
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Proteins,
72,
1333-1351.
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A.Bartels,
F.Forlani,
S.Pagani,
and
J.Papenbrock
(2007).
Conformational studies on Arabidopsis sulfurtransferase AtStr1 with spectroscopic methods.
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Biol Chem,
388,
53-59.
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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
codes are
shown on the right.
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Links
