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PDBsum entry 3f9y

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protein ligands Protein-protein interface(s) links
Transferase PDB id
3f9y
Jmol PyMol
Contents
Protein chains
159 a.a. *
Ligands
LYS-ARG-HIS-ARG-
MLZ-VAL-LEU
LYS-ARG-HIS-ARG-
MLZ-VAL-LEU-ARG
SAH ×2
Waters ×227
* Residue conservation analysis
PDB id:
3f9y
Name: Transferase
Title: Structural insights into lysine multiple methylation by set methyltransferases, set8-y334f / h4-lys20me1 / adohcy
Structure: Histone-lysine n-methyltransferase setd8. Chain: a, b. Fragment: set domain: unp residues 232-393. Synonym: h4-k20-hmtase setd8, set domain-containing protein domain-containing protein 07, pr/set07, pr-set7, lysine n- methyltransferase 5a. Engineered: yes. Mutation: yes. Histone h4.
Source: Homo sapiens. Organism_taxid: 9606. Gene: setd8, kmt5a, prset7, set07, set8. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: synthetic peptide corresponding to residues human histone h4
Resolution:
1.50Å     R-factor:   0.195     R-free:   0.220
Authors: J-F.Couture,L.M.A.Dirk,J.S.Brunzelle,R.L.Houtz,R.C.Trievel
Key ref:
J.F.Couture et al. (2008). Structural origins for the product specificity of SET domain protein methyltransferases. Proc Natl Acad Sci U S A, 105, 20659-20664. PubMed id: 19088188 DOI: 10.1073/pnas.0806712105
Date:
14-Nov-08     Release date:   25-Nov-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9NQR1  (SETD8_HUMAN) -  N-lysine methyltransferase SETD8
Seq:
Struc:
393 a.a.
159 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.1.1.43  - Histone-lysine N-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N6-methyl-L-lysine-[histone]
S-adenosyl-L-methionine
+ L-lysine-[histone]
=
S-adenosyl-L-homocysteine
Bound ligand (Het Group name = SAH)
corresponds exactly
+ N(6)-methyl-L-lysine-[histone]
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     histone-lysine N-methyltransferase activity     1 term  

 

 
    Added reference    
 
 
DOI no: 10.1073/pnas.0806712105 Proc Natl Acad Sci U S A 105:20659-20664 (2008)
PubMed id: 19088188  
 
 
Structural origins for the product specificity of SET domain protein methyltransferases.
J.F.Couture, L.M.Dirk, J.S.Brunzelle, R.L.Houtz, R.C.Trievel.
 
  ABSTRACT  
 
SET domain protein lysine methyltransferases (PKMTs) regulate transcription and other cellular functions through site-specific methylation of histones and other substrates. PKMTs catalyze the formation of monomethylated, dimethylated, or trimethylated products, establishing an additional hierarchy with respect to methyllysine recognition in signaling. Biochemical studies of PKMTs have identified a conserved position within their active sites, the Phe/Tyr switch, that governs their respective product specificities. To elucidate the mechanism underlying this switch, we have characterized a Phe/Tyr switch mutant of the histone H4 Lys-20 (H4K20) methyltransferase SET8, which alters its specificity from a monomethyltransferase to a dimethyltransferase. The crystal structures of the SET8 Y334F mutant bound to histone H4 peptides bearing unmodified, monomethyl, and dimethyl Lys-20 reveal that the phenylalanine substitution attenuates hydrogen bonding to a structurally conserved water molecule adjacent to the Phe/Tyr switch, facilitating its dissociation. The additional space generated by the solvent's dissociation enables the monomethyllysyl side chain to adopt a conformation that is catalytically competent for dimethylation and furnishes sufficient volume to accommodate the dimethyl epsilon-ammonium product. Collectively, these results indicate that the Phe/Tyr switch regulates product specificity through altering the affinity of an active-site water molecule whose dissociation is required for lysine multiple methylation.
 
  Selected figure(s)  
 
Figure 2.
Structures of the active sites of native SET8 and the Y334F mutant bound to AdoHcy and H4K20, H4K20me1, and H4K20me2 peptides. His-18 in histone H4 forms 1 wall of the channel and was omitted to provide an unobstructed view of the active site. SET8, histone H4, and AdoHcy are delineated by gray, gold, and green carbon atoms, respectively. The Y334F mutation is highlighted in magenta. (Insets) Shown are the F[O] − F[C] omit map electron densities for the various K20 side chains contoured at 2.0 σ. Conventional and CH^…O hydrogen bonds are depicted as orange and cyan dashes, respectively. (A) Native SET8–H4K20–AdoHcy complex (Protein Data Bank ID code 1ZKK). (B) SET8 Y334F–H4K20–AdoHcy. (C) SET8 Y334F–H4K20me1–AdoHcy. (D) SET8 Y334F–H4K20me2–AdoHcy.
Figure 4.
Model for H4K20 dimethylation by the SET8 Y334F mutant. (A) First methyltransfer reaction. In the SET8 Y334F–H4K20–AdoMet complex, AdoMet was modeled in the active site by using the AdoHcy coordinates (Fig. 2 color scheme with hydrogens rendered in cyan). The S[N]2 reaction distance and bond angle corresponding to the H4K20 ε-amine group and the AdoMet methyl group and sulfonium cation are noted. Fig. S6 illustrates the hydrogen bonding to the K20 ε-amine. (B) Second methyltransfer reaction. In this substrate complex, the H4K20me1 side chain is modeled with its methyl group projecting into the vacated water binding site, which is inferred from the coordinates of the corresponding methyl group in the H4K20me2 product complex (Fig. 2D). This orientation aligns the K20me1 ε-amine for methyltransfer with AdoMet.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21276944 A.Dhayalan, S.Kudithipudi, P.Rathert, and A.Jeltsch (2011).
Specificity analysis-based identification of new methylation targets of the SET7/9 protein lysine methyltransferase.
  Chem Biol, 18, 111-120.  
  21141727 A.K.Upadhyay, and X.Cheng (2011).
Dynamics of histone lysine methylation: structures of methyl writers and erasers.
  Prog Drug Res, 67, 107-124.  
21243713 S.Krishnan, S.Horowitz, and R.C.Trievel (2011).
Structure and function of histone H3 lysine 9 methyltransferases and demethylases.
  Chembiochem, 12, 254-263.  
20084102 H.Wu, J.Min, V.V.Lunin, T.Antoshenko, L.Dombrovski, H.Zeng, A.Allali-Hassani, V.Campagna-Slater, M.Vedadi, C.H.Arrowsmith, A.N.Plotnikov, and M.Schapira (2010).
Structural biology of human H3K9 methyltransferases.
  PLoS One, 5, e8570.
PDB codes: 2igq 2o8j 2qpw 2r3a 2rfi 3hna
21206904 L.W.Tsang, N.Hu, and D.A.Underhill (2010).
Comparative analyses of SUV420H1 isoforms and SUV420H2 reveal differences in their cellular localization and effects on myogenic differentiation.
  PLoS One, 5, e14447.  
20081860 R.D.Morin, N.A.Johnson, T.M.Severson, A.J.Mungall, J.An, R.Goya, J.E.Paul, M.Boyle, B.W.Woolcock, F.Kuchenbauer, D.Yap, R.K.Humphries, O.L.Griffith, S.Shah, H.Zhu, M.Kimbara, P.Shashkin, J.F.Charlot, M.Tcherpakov, R.Corbett, A.Tam, R.Varhol, D.Smailus, M.Moksa, Y.Zhao, A.Delaney, H.Qian, I.Birol, J.Schein, R.Moore, R.Holt, D.E.Horsman, J.M.Connors, S.Jones, S.Aparicio, M.Hirst, R.D.Gascoyne, and M.A.Marra (2010).
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin.
  Nat Genet, 42, 181-185.  
21062871 T.Sahr, T.Adam, C.Fizames, C.Maurel, and V.Santoni (2010).
O-carboxyl- and N-methyltransferases active on plant aquaporins.
  Plant Cell Physiol, 51, 2092-2104.  
19822661 J.N.Psathas, S.Zheng, S.Tan, and J.C.Reese (2009).
Set2-dependent K36 methylation is regulated by novel intratail interactions within H3.
  Mol Cell Biol, 29, 6413-6426.  
19882600 Q.Xu, Y.Z.Chu, H.B.Guo, J.C.Smith, and H.Guo (2009).
Energy triplets for writing epigenetic marks: insights from QM/MM free-energy simulations of protein lysine methyltransferases.
  Chemistry, 15, 12596-12599.  
  20582239 T.Petrossian, and S.Clarke (2009).
Bioinformatic Identification of Novel Methyltransferases.
  Epigenomics, 1, 163-175.  
19398585 Y.H.Takahashi, J.S.Lee, S.K.Swanson, A.Saraf, L.Florens, M.P.Washburn, R.C.Trievel, and A.Shilatifard (2009).
Regulation of H3K4 trimethylation via Cps40 (Spp1) of COMPASS is monoubiquitination independent: implication for a Phe/Tyr switch by the catalytic domain of Set1.
  Mol Cell Biol, 29, 3478-3486.  
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.

 

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