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PDBsum entry 1jw3
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Structural genomics, unknown function PDB id
1jw3

 

 

 

 

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Contents
Protein chain
140 a.a. *
* Residue conservation analysis
PDB id:
1jw3
Name: Structural genomics, unknown function
Title: Solution structure of methanobacterium thermoautotrophicum protein 1598. Ontario centre for structural proteomics target mth1598_1_140; northeast structural genomics target tt6
Structure: Conserved hypothetical protein mth1598. Chain: a
Source: Methanothermobacter thermautotrophicus. Organism_taxid: 145262. Plasmid: pet15b
NMR struc: 10 models
Authors: X.Chang,G.Connelly,A.Yee,M.A.Kennedy,A.M.Edwards,C.H.Arrowsmith, Northeast Structural Genomics Consortium (Nesg)
Key ref:
A.Yee et al. (2002). An NMR approach to structural proteomics. Proc Natl Acad Sci U S A, 99, 1825-1830. PubMed id: 11854485 DOI: 10.1073/pnas.042684599
Date:
02-Sep-01     Release date:   27-Feb-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O27635  (ARCH_METTH) -  Protein archease from Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Seq:
Struc: 		140 a.a.
140 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1073/pnas.042684599 Proc Natl Acad Sci U S A 99:1825-1830 (2002)
PubMed id: 11854485  
 
 
An NMR approach to structural proteomics.
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.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Histogram of the number of proteins cloned (blue), expressed (red), and soluble (gray) from each organism. 		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).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Structural proteomics by NMR spectroscopy.
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Crystal structure of a novel Thermotoga maritima enzyme (TM1112) from the cupin family at 1.83 A resolution.
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15152082 F.J.Blanco, A.Yee, R.Campos-Olivas, A.R.Ortiz, D.Devos, A.Valencia, C.H.Arrowsmith, and M.Rico (2004).
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  Protein Sci, 13, 1458-1465.
PDB code: 1pu1
15162483 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.  
15479237 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.
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Sonication of proteins causes formation of aggregates that resemble amyloid.
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15281131 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.  
12634795 A.Sali, R.Glaeser, T.Earnest, and W.Baumeister (2003).
From words to literature in structural proteomics.
  Nature, 422, 216-225.  
12557182 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.
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12824322 A.Stark, and R.B.Russell (2003).
Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.
  Nucleic Acids Res, 31, 3341-3344.  
14627743 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.
  Protein Sci, 12, 2831-2837.
PDB code: 1ne3
12547423 C.Zhang, and S.H.Kim (2003).
Overview of structural genomics: from structure to function.
  Curr Opin Chem Biol, 7, 28-32.  
14506850 D.Frishman (2003).
What we have learned about prokaryotes from structural genomics.
  OMICS, 7, 211-224.  
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Refolding out of guanidine hydrochloride is an effective approach for high-throughput structural studies of small proteins.
  Protein Sci, 12, 2073-2080.  
12948670 P.Braun, and J.LaBaer (2003).
High throughput protein production for functional proteomics.
  Trends Biotechnol, 21, 383-388.  
12547425 S.Yokoyama (2003).
Protein expression systems for structural genomics and proteomics.
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12211008 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.
  Proteins, 49, 289-293.
PDB code: 1lv3
12142361 V.Reinke, and K.P.White (2002).
Developmental genomic approaches in model organisms.
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  18629268 , (2002).
Current awareness on comparative and functional genomics.
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Structural proteomics: the potential of high-throughput structure determination.
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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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