PDBsum entry 1nv9

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Transferase PDB id
Protein chain
264 a.a. *
Waters ×20
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Hemk, apo structure
Structure: Hemk protein. Chain: a. Fragment: hemk. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: hemk. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.36Å     R-factor:   0.242     R-free:   0.300
Authors: H.L.Schubert,J.D.Phillips,C.P.Hill
Key ref:
H.L.Schubert et al. (2003). Structures along the catalytic pathway of PrmC/HemK, an N5-glutamine AdoMet-dependent methyltransferase. Biochemistry, 42, 5592-5599. PubMed id: 12741815 DOI: 10.1021/bi034026p
02-Feb-03     Release date:   27-May-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9WYV8  (PRMC_THEMA) -  Release factor glutamine methyltransferase
282 a.a.
264 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Peptide chain release factor N(5)-glutamine methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-adenosyl-L-methionine + [peptide chain release factor 1 or 2]-L- glutamine = S-adenosyl-L-homocysteine + [peptide chain release factor 1 or 2]-N5-methyl-L-glutamine
+ [peptide chain release factor 1 or 2]-L- glutamine
= S-adenosyl-L-homocysteine
+ [peptide chain release factor 1 or 2]-N(5)-methyl-L-glutamine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     methylation   3 terms 
  Biochemical function     protein-glutamine N-methyltransferase activity     5 terms  


    Added reference    
DOI no: 10.1021/bi034026p Biochemistry 42:5592-5599 (2003)
PubMed id: 12741815  
Structures along the catalytic pathway of PrmC/HemK, an N5-glutamine AdoMet-dependent methyltransferase.
H.L.Schubert, J.D.Phillips, C.P.Hill.
Posttranslational methylation of release factors on the glutamine residue of a conserved GGQ motif is required for efficient termination of protein synthesis. This methylation is performed by an N(5)-glutamine methyltransferase called PrmC/HemK, whose crystal structure we report here at 2.2 A resolution. The electron density at the active site appears to contain a mixture of the substrates, S-adenosyl-L-methionine (AdoMet) and glutamine, and the products, S-adenosyl-L-homocysteine (AdoHcy) and N(5)-methylglutamine. The C-terminal domain of PrmC adopts the canonical AdoMet-dependent methyltransferase fold and shares structural similarity with the nucleotide N-methyltransferases in the active site, including use of a conserved (D/N)PPY motif to select and position the glutamine substrate. Residues of the PrmC (197)NPPY(200) motif form hydrogen bonds that position the planar Gln side chain such that the lone-pair electrons on the nitrogen nucleophile are oriented toward the methyl group of AdoMet. In the product complex, the methyl group remains pointing toward the sulfur, consistent with either an sp(3)-hybridized, positively charged Gln nitrogen, or a neutral sp(2)-hybridized nitrogen in a strained conformation. Due to steric overlap within the active site, proton loss and formation of the neutral planar methylamide product are likely to occur during or after product release. These structures, therefore, represent intermediates along the catalytic pathway of PrmC and show how the (D/N)PPY motif can be used to select a wide variety substrates.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19116772 D.S.Nie, Y.B.Liu, and G.X.Lu (2009).
Cloning and primarily function study of two novel putative N5-glutamine methyltransferase (Hemk) splice variants from mouse stem cells.
  Mol Biol Rep, 36, 2221-2228.  
19285505 H.Demirci, R.Belardinelli, E.Seri, S.T.Gregory, C.Gualerzi, A.E.Dahlberg, and G.Jogl (2009).
Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine.
  J Mol Biol, 388, 271-282.
PDB codes: 3fut 3fuu 3fuv 3fuw 3fux
19351663 T.C.Petrossian, and S.G.Clarke (2009).
Multiple Motif Scanning to identify methyltransferases from the yeast proteome.
  Mol Cell Proteomics, 8, 1516-1526.  
18389380 Y.Liu, D.Nie, Y.Huang, and G.Lu (2009).
RNAi-mediated knock-down of gene mN6A1 reduces cell proliferation and decreases protein translation.
  Mol Biol Rep, 36, 767-774.  
18252828 B.P.Anton, L.Saleh, J.S.Benner, E.A.Raleigh, S.Kasif, and R.J.Roberts (2008).
RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli.
  Proc Natl Acad Sci U S A, 105, 1826-1831.  
18469097 G.Shen, H.S.Leonard, W.M.Schluchter, and D.A.Bryant (2008).
CpcM posttranslationally methylates asparagine-71/72 of phycobiliprotein beta subunits in Synechococcus sp. strain PCC 7002 and Synechocystis sp. strain PCC 6803.
  J Bacteriol, 190, 4808-4817.  
18667428 H.Demirci, S.T.Gregory, A.E.Dahlberg, and G.Jogl (2008).
Crystal structure of the Thermus thermophilus 16 S rRNA methyltransferase RsmC in complex with cofactor and substrate guanosine.
  J Biol Chem, 283, 26548-26556.
PDB codes: 3dmf 3dmg 3dmh
18611379 H.Demirci, S.T.Gregory, A.E.Dahlberg, and G.Jogl (2008).
Multiple-site trimethylation of ribosomal protein L11 by the PrmA methyltransferase.
  Structure, 16, 1059-1066.
PDB codes: 3cjq 3cjr 3cjs 3cjt 3cju 3egv
18247349 R.Agarwal, S.K.Burley, and S.Swaminathan (2008).
A novel mode of dimerization via formation of a glutamate anhydride crosslink in a protein crystal structure.
  Proteins, 71, 1038-1041.
PDB code: 1sg9
17591721 R.Wu, and Z.Cao (2008).
QM/MM study of catalytic methyl transfer by the N(5)-glutamine SAM-dependent methyltransferase and its inhibition by the nitrogen analogue of coenzyme.
  J Comput Chem, 29, 350-357.  
18484748 Y.Peng, Q.Feng, D.Wilk, A.A.Adjei, O.E.Salavaggione, R.M.Weinshilboum, and V.C.Yee (2008).
Structural basis of substrate recognition in thiopurine s-methyltransferase.
  Biochemistry, 47, 6216-6225.
PDB codes: 3bgd 3bgi
17610498 B.Polevoda, and F.Sherman (2007).
Methylation of proteins involved in translation.
  Mol Microbiol, 65, 590-606.  
17671979 C.Wang, O.Schueler-Furman, I.Andre, N.London, S.J.Fleishman, P.Bradley, B.Qian, and D.Baker (2007).
RosettaDock in CAPRI rounds 6-12.
  Proteins, 69, 758-763.  
17215866 H.Demirci, S.T.Gregory, A.E.Dahlberg, and G.Jogl (2007).
Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA.
  EMBO J, 26, 567-577.
PDB codes: 2nxc 2nxe 2nxj 2nxn
17803212 K.Wiehe, B.Pierce, W.W.Tong, H.Hwang, J.Mintseris, and Z.Weng (2007).
The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI.
  Proteins, 69, 719-725.  
17894347 S.Chaudhury, A.Sircar, A.Sivasubramanian, M.Berrondo, and J.J.Gray (2007).
Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12.
  Proteins, 69, 793-800.  
16321977 B.Polevoda, L.Span, and F.Sherman (2006).
The yeast translation release factors Mrf1p and Sup45p (eRF1) are methylated, respectively, by the methyltransferases Mtq1p and Mtq2p.
  J Biol Chem, 281, 2562-2571.  
16885288 M.Watanabe, H.Yuzawa, N.Handa, and I.Kobayashi (2006).
Hyperthermophilic DNA methyltransferase M.PabI from the archaeon Pyrococcus abyssi.
  Appl Environ Microbiol, 72, 5367-5375.  
15789416 E.Purta, F.van Vliet, C.Tricot, L.G.De Bie, M.Feder, K.Skowronek, L.Droogmans, and J.M.Bujnicki (2005).
Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis.
  Proteins, 59, 482-488.  
16364916 M.Graille, V.Heurgué-Hamard, S.Champ, L.Mora, N.Scrima, N.Ulryck, H.van Tilbeurgh, and R.H.Buckingham (2005).
Molecular basis for bacterial class I release factor methylation by PrmC.
  Mol Cell, 20, 917-927.
PDB code: 2b3t
15509572 V.Heurgué-Hamard, S.Champ, L.Mora, T.Merkulova-Rainon, T.Merkoulova-Rainon, L.L.Kisselev, and R.H.Buckingham (2005).
The glutamine residue of the conserved GGQ motif in Saccharomyces cerevisiae release factor eRF1 is methylated by the product of the YDR140w gene.
  J Biol Chem, 280, 2439-2445.  
16260766 W.Sun, X.Xu, M.Pavlova, A.M.Edwards, A.Joachimiak, A.Savchenko, and D.Christendat (2005).
The crystal structure of a novel SAM-dependent methyltransferase PH1915 from Pyrococcus horikoshii.
  Protein Sci, 14, 3121-3128.
PDB code: 2as0
15869391 X.Cheng, R.E.Collins, and X.Zhang (2005).
Structural and sequence motifs of protein (histone) methylation enzymes.
  Annu Rev Biophys Biomol Struct, 34, 267-294.  
15629922 Y.Pannekoek, V.Heurgué-Hamard, A.A.Langerak, D.Speijer, R.H.Buckingham, and A.van der Ende (2005).
The N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase PrmC/HemK in Chlamydia trachomatis methylates class 1 release factors.
  J Bacteriol, 187, 507-511.  
15292170 K.Sawada, Z.Yang, J.R.Horton, R.E.Collins, X.Zhang, and X.Cheng (2004).
Structure of the conserved core of the yeast Dot1p, a nucleosomal histone H3 lysine 79 methyltransferase.
  J Biol Chem, 279, 43296-43306.
PDB code: 1u2z
15223314 Z.Yang, L.Shipman, M.Zhang, B.P.Anton, R.J.Roberts, and X.Cheng (2004).
Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase.
  J Mol Biol, 340, 695-706.
PDB code: 1t43
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.