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PDBsum entry 2vdu
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protein ligands Protein-protein interface(s) links
Transferase PDB id
2vdu

 

 

 

 

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Contents
Protein chains
374 a.a. *
201 a.a. *
Ligands
PO4 ×2
Waters ×259
* Residue conservation analysis
PDB id:
2vdu
Name: Transferase
Title: Structure of trm8-trm82, the yeast tRNA m7g methylation complex
Structure: tRNA (guanine-n(7)-)-methyltransferase-associated wd repeat protein trm82. Chain: b, d. Engineered: yes. tRNA (guanine-n(7)-)-methyltransferase. Chain: e, f. Fragment: 46-end, residues 39-286. Synonym: trm8, tRNA(m7g46)-methyltransferase. Engineered: yes.
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.40Å     R-factor:   0.228     R-free:   0.276
Authors: N.Leulliot,M.Chaillet,D.Durand,N.Ulryck,K.Blondeau,H.Van Tilbeurgh
Key ref:
N.Leulliot et al. (2008). Structure of the yeast tRNA m7G methylation complex. Structure, 16, 52-61. PubMed id: 18184583 DOI: 10.1016/j.str.2007.10.025
Date:
11-Oct-07     Release date:   18-Dec-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q03774  (TRM82_YEAST) -  tRNA (guanine-N(7)-)-methyltransferase non-catalytic subunit TRM82 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		444 a.a.
374 a.a.
Protein chains
Pfam   ArchSchema ?
Q12009  (TRMB_YEAST) -  tRNA (guanine-N(7)-)-methyltransferase from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		286 a.a.
201 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: Chains B, D: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
   Enzyme class 2: Chains E, F: E.C.2.1.1.33  - tRNA (guanine(46)-N(7))-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: guanosine46 in tRNA + S-adenosyl-L-methionine = N7- methylguanosine46 in tRNA + S-adenosyl-L-homocysteine
guanosine(46) in tRNA
 + S-adenosyl-L-methionine
 = N(7)- methylguanosine(46) in tRNA
 + S-adenosyl-L-homocysteine
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Added reference    
 
 
DOI no: 10.1016/j.str.2007.10.025 Structure 16:52-61 (2008)
PubMed id: 18184583  
 
 
Structure of the yeast tRNA m7G methylation complex.
N.Leulliot, M.Chaillet, D.Durand, N.Ulryck, K.Blondeau, H.van Tilbeurgh.
 
  ABSTRACT  
 
Loss of N7-methylguanosine (m7G) modification is involved in the recently discovered rapid tRNA degradation pathway. In yeast, this modification is catalyzed by the heterodimeric complex composed of a catalytic subunit Trm8 and a noncatalytic subunit Trm82. We have solved the crystal structure of Trm8 alone and in complex with Trm82. Trm8 undergoes subtle conformational changes upon Trm82 binding which explains the requirement of Trm82 for activity. Cocrystallization with the S-adenosyl-methionine methyl donor defines the putative catalytic site and a guanine binding pocket. Small-angle X-ray scattering in solution of the Trm8-Trm82 heterodimer in complex with tRNA(Phe) has enabled us to propose a low-resolution structure of the ternary complex which defines the tRNA binding mode of Trm8-Trm82 and the structural elements contributing to specificity.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Structure of the Trm8-Trm82 Complex
(A) Cartoon representation of the Trm8-Trm82 complex. The Trm8-specific insertions to the methyltransferase fold are colored red. The α3 helix and AdoMet cofactor, not observable in the complex but present in the free Trm8 structure, are shown. The β4-αD loop has been modeled using the BsTrmB structure as a reference.
(B and C) Surface representation of the Trm8-Trm82 complex in the same orientation as (A). The surface in (B) is colored in increasing shades of red reflecting increasing residue conservation. The electrostatic potential in (C) is colored on the surface of the protein from red (negative) to blue (positive). Figures were generated using PyMOL (DeLano, 2002). 		Figure 4.
Figure 4. Model of the Trm8-Trm82-tRNA^Phe Complex
(A) SAXS curve of the Trm8-Trm82-tRNA^Phe complex (model 1). Black and red curves are experimental and calculated, respectively.
(B) Model of the Trm8-Trm82-tRNA^Phe complex in the same orientation as Figure 1A. The represented model corresponds to model 1. A schematic representation of the tRNA with the color code used is shown in the inset.
(C) Interaction of the β4-αD loop with the tRNA in model 3. Trm82 is shown with a transparent surface on the right.
 
  The above figures are reprinted by permission from Cell Press: Structure (2008, 16, 52-61) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19906721 A.Nakamura, K.Sheppard, J.Yamane, M.Yao, D.Söll, and I.Tanaka (2010).
Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition.
  Nucleic Acids Res, 38, 672-682.
PDB code: 3ip4
20535822 A.Sircar, S.Chaudhury, K.P.Kilambi, M.Berrondo, and J.J.Gray (2010).
A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19.
  Proteins, 78, 3115-3123.  
20602351 C.Pons, A.Solernou, L.Perez-Cano, S.Grosdidier, and J.Fernandez-Recio (2010).
Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain-domain assembly and protein-RNA binding.
  Proteins, 78, 3182-3188.  
19934251 C.Tomikawa, T.Yokogawa, T.Kanai, and H.Hori (2010).
N7-Methylguanine at position 46 (m7G46) in tRNA from Thermus thermophilus is required for cell viability at high temperatures through a tRNA modification network.
  Nucleic Acids Res, 38, 942-957.  
20607855 E.Mashiach, D.Schneidman-Duhovny, A.Peri, Y.Shavit, R.Nussinov, and H.J.Wolfson (2010).
An integrated suite of fast docking algorithms.
  Proteins, 78, 3197-3204.  
20936681 H.Hwang, T.Vreven, B.G.Pierce, J.H.Hung, and Z.Weng (2010).
Performance of ZDOCK and ZRANK in CAPRI rounds 13-19.
  Proteins, 78, 3104-3110.  
20512115 H.Walbott, S.Mouffok, R.Capeyrou, S.Lebaron, O.Humbert, H.van Tilbeurgh, Y.Henry, and N.Leulliot (2010).
Prp43p contains a processive helicase structural architecture with a specific regulatory domain.
  EMBO J, 29, 2194-2204.
PDB code: 2xau
20589643 J.Janin (2010).
The targets of CAPRI Rounds 13-19.
  Proteins, 78, 3067-3072.  
20665475 M.Bueno, N.A.Temiz, and C.J.Camacho (2010).
Novel modulation factor quantifies the role of water molecules in protein interactions.
  Proteins, 78, 3226-3234.  
20607697 M.Eisenstein, A.Ben-Shimon, Z.Frankenstein, and N.Kowalsman (2010).
CAPRI targets T29-T42: proving ground for new docking procedures.
  Proteins, 78, 3174-3181.  
20806235 M.F.Lensink, and S.J.Wodak (2010).
Docking and scoring protein interactions: CAPRI 2009.
  Proteins, 78, 3073-3084.  
20839234 M.F.Lensink, and S.J.Wodak (2010).
Blind predictions of protein interfaces by docking calculations in CAPRI.
  Proteins, 78, 3085-3095.  
20715290 S.Fiorucci, and M.Zacharias (2010).
Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT.
  Proteins, 78, 3131-3139.  
20718048 S.J.de Vries, A.S.Melquiond, P.L.Kastritis, E.Karaca, A.Bordogna, M.van Dijk, J.P.Rodrigues, and A.M.Bonvin (2010).
Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions.
  Proteins, 78, 3242-3249.  
20589642 S.Qin, and H.X.Zhou (2010).
Selection of near-native poses in CAPRI rounds 13-19.
  Proteins, 78, 3166-3173.  
19373903 H.Zhou, Q.Liu, W.Yang, Y.Gao, M.Teng, and L.Niu (2009).
Monomeric tRNA (m(7)G46) methyltransferase from Escherichia coli presents a novel structure at the function-essential insertion.
  Proteins, 76, 512-515.
PDB codes: 3dxx 3dxy 3dxz
19452551 N.Kowalsman, and M.Eisenstein (2009).
Combining interface core and whole interface descriptors in postscan processing of protein-protein docking models.
  Proteins, 77, 297-318.  
18978353 S.Quevillon-Cheruel, N.Leulliot, C.A.Muniz, M.Vincent, J.Gallay, M.Argentini, D.Cornu, F.Boccard, B.Lemaître, and H.van Tilbeurgh (2009).
Evf, a virulence factor produced by the Drosophila pathogen Erwinia carotovora, is an S-palmitoylated protein with a new fold that binds to lipid vesicles.
  J Biol Chem, 284, 3552-3562.
PDB code: 2w3y
  18678947 Q.Liu, Y.Gao, W.Yang, H.Zhou, Y.Gao, X.Zhang, M.Teng, and L.Niu (2008).
Crystallization and preliminary crystallographic analysis of tRNA (m(7)G46) methyltransferase from Escherichia coli.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 743-745.  
18974182 X.Yang, M.Morita, H.Wang, T.Suzuki, W.Yang, Y.Luo, C.Zhao, Y.Yu, M.Bartlam, T.Yamamoto, and Z.Rao (2008).
Crystal structures of human BTG2 and mouse TIS21 involved in suppression of CAF1 deadenylase activity.
  Nucleic Acids Res, 36, 6872-6881.
PDB codes: 3djn 3dju
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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