PDBsum entry 1vee

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Structural genomics, unknown function PDB id
Protein chain
134 a.a. *
* Residue conservation analysis
PDB id:
Name: Structural genomics, unknown function
Title: Nmr structure of the hypothetical rhodanese domain at4g01050 from arabidopsis thaliana
Structure: Proline-rich protein family. Chain: a. Fragment: rhodanese hypothetical domain. Synonym: hypothetical protein rafl06-68-j04. Engineered: yes
Source: Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: riken cdna rafl06-68-j04. Other_details: e.Coli cell-free protein synthesis
NMR struc: 20 models
Authors: 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)
Key ref:
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: 15576557 DOI: 10.1110/ps.041138705
30-Mar-04     Release date:   25-Jan-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9M158  (STR4_ARATH) -  Rhodanese-like domain-containing protein 4, chloroplastic
466 a.a.
134 a.a.*
Key:    PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 12 residue positions (black crosses)


DOI no: 10.1110/ps.041138705 Protein Sci 14:224-230 (2005)
PubMed id: 15576557  
Solution structure of the rhodanese homology domain At4g01050(175-295) from Arabidopsis thaliana.
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.
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.
  Selected figure(s)  
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.
  The above figure is reprinted by permission from the Protein Society: Protein Sci (2005, 14, 224-230) copyright 2005.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20135153 J.Papenbrock, S.Guretzki, and M.Henne (2011).
Latest news about the sulfurtransferase protein family of higher plants.
  Amino Acids, 41, 43-57.  
19820233 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.
  J Biol Chem, 284, 35612-35620.
PDB codes: 2kmo 2kmp 2kmq 2kmr
18807026 P.Güntert (2009).
Automated structure determination from NMR spectra.
  Eur Biophys J, 38, 129-143.  
19682289 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.
  Plant J, 60, 783-794.  
18384072 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.
  Proteins, 72, 1333-1351.  
17214549 A.Bartels, F.Forlani, S.Pagani, and J.Papenbrock (2007).
Conformational studies on Arabidopsis sulfurtransferase AtStr1 with spectroscopic methods.
  Biol Chem, 388, 53-59.  
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