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PDBsum entry 1b29

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protein links
Oxidoreductase PDB id
1b29
Jmol
Contents
Protein chain
385 a.a.
Theoretical model
PDB id:
1b29
Name: Oxidoreductase
Title: Glutamyl tRNA reductase from hordeum vulgare
Structure: Glutamyl tRNA reductase. Chain: a. Ec: 1.2.1.-
Source: Hordeum vulgare. Barley. Organ: leaf. Tissue: mesophyll. Organelle: chloroplast. Cellular_location: chloroplast
Authors: S.S.Brody,S.Gough,G.Kannangara
Key ref:
S.S.Brody et al. (1999). Predicted structure and fold recognition for the glutamyl tRNA reductase family of proteins. Proteins, 37, 485-493. PubMed id: 10591107 DOI: 10.1002/(SICI)1097-0134(19991115)37:3<485::AID-PROT15>3.0.CO;2-G
Date:
18-Nov-98     Release date:   09-Dec-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q42843  (HEM11_HORVU) -  Glutamyl-tRNA reductase 1, chloroplastic
Seq:
Struc:
 
Seq:
Struc:
527 a.a.
385 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.1.2.1.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1002/(SICI)1097-0134(19991115)37:3<485::AID-PROT15>3.0.CO;2-G Proteins 37:485-493 (1999)
PubMed id: 10591107  
 
 
Predicted structure and fold recognition for the glutamyl tRNA reductase family of proteins.
S.S.Brody, S.P.Gough, C.G.Kannangara.
 
  ABSTRACT  
 
The conserved residues of glutamyl tRNA reductase (GTR) from Hordeum vulgare (GTRhorvu) were found from an alignment/pile-up of 24 homologous sequences found using BLAST searches. A multiple alignment of sequences was used to obtain a prediction of the secondary structure of the GTR's. This secondary structure was submitted to the THREADER program to find possible homologous 3D structures. To help select the template for predicting the fold for GTRhorvu, we employed both molecular-biological and biochemical information about GTRhorvu. After fitting the secondary structure of GTRhorvu to the selected template, the MODELLER program was used to determine the fold for GTRhorvu. This model was built using the B subunit of succinyl CoA synthetase, 1scuB, as a template for the 3D structure of GTRhorvu. From the predicted structure, possible regions were identified for the binding of glutamyl-tRNA, NADPH and a heme inhibitor. The predicted structure was used to propose a detailed biochemical mechanism for the GTR, involving Mg catalyzed thioester formation and reduction by NADPH to glutamate-1-semialdehyde. Sites for these reactions are identified. The predicted structure has been deposited in the Brookhaven database as ID 1b61.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The role of glutamyl tRNA reductase in the biosynthesis of metalloporphyrins.
Figure 3.
Figure 3. The secondary structure of GTRhorvu based on a multiple alignment of homologous sequences.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (1999, 37, 485-493) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21161598 R.E.Hirsch, M.Rich, and Govindjee (2010).
A tribute to Seymour Steven Brody: in memoriam (November 29, 1927 to May 25, 2010).
  Photosynth Res, 106, 191-199.  
16957991 J.Ruan, K.Chen, J.A.Tuszynski, and L.A.Kurgan (2006).
Quantitative analysis of the conservation of the tertiary structure of protein segments.
  Protein J, 25, 301-315.  
15531590 K.M.Mayer, and J.Shanklin (2005).
A structural model of the plant acyl-acyl carrier protein thioesterase FatB comprises two helix/4-stranded sheet domains, the N-terminal domain containing residues that affect specificity and the C-terminal domain containing catalytic residues.
  J Biol Chem, 280, 3621-3627.
PDB code: 1xxy
16215169 Z.Vasileuskaya, U.Oster, and C.F.Beck (2005).
Mg-protoporphyrin IX and heme control HEMA, the gene encoding the first specific step of tetrapyrrole biosynthesis, in Chlamydomonas reinhardtii.
  Eukaryot Cell, 4, 1620-1628.  
15568974 A.R.Grossman, M.Lohr, and C.S.Im (2004).
Chlamydomonas reinhardtii in the landscape of pigments.
  Annu Rev Genet, 38, 119-173.  
15584960 D.Goslings, R.Meskauskiene, C.Kim, K.P.Lee, M.Nater, and K.Apel (2004).
Concurrent interactions of heme and FLU with Glu tRNA reductase (HEMA1), the target of metabolic feedback inhibition of tetrapyrrole biosynthesis, in dark- and light-grown Arabidopsis plants.
  Plant J, 40, 957-967.  
11726494 J.Moser, W.D.Schubert, V.Beier, I.Bringemeier, D.Jahn, and D.W.Heinz (2001).
V-shaped structure of glutamyl-tRNA reductase, the first enzyme of tRNA-dependent tetrapyrrole biosynthesis.
  EMBO J, 20, 6583-6590.
PDB code: 1gpj
11391772 L.M.Brown, R.A.Gonzalez, J.Novotny, and S.J.Flint (2001).
Structure of the adenovirus E4 Orf6 protein predicted by fold recognition and comparative protein modeling.
  Proteins, 44, 97.  
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.