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PDBsum entry 3f70
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protein ligands Protein-protein interface(s) links
Transcription regulator PDB id
3f70

 

 

 

 

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Contents
Protein chains
392 a.a. *
410 a.a. *
Ligands
MLZ ×2
Waters ×290
* Residue conservation analysis
PDB id:
3f70
Name: Transcription regulator
Title: Crystal structure of l3mbtl2-h4k20me1 complex
Structure: Lethal(3)malignant brain tumor-like 2 protein. Chain: a, b. Synonym: l(3)mbt-like 2 protein, h-l(3)mbt-like protein. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: l3mbtl2. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.10Å     R-factor:   0.203     R-free:   0.268
Authors: Y.Guo,C.Qi,A.Allali-Hassani,P.Pan,H.Zhu,A.Dong,F.Mackenzie,L.Crombet, P.Loppnau,I.Kozieradzki,M.Vedadi,A.M.Edwards,J.Weigelt,C.Bountra, C.H.Arrowsmith,A.Botchkarev,R.Read,J.Min,Structural Genomics Consortium (Sgc)
Key ref: Y.Guo et al. (2009). Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2. Nucleic Acids Res, 37, 2204-2210. PubMed id: 19233876
Date:
07-Nov-08     Release date:   06-Jan-09    
Supersedes: 3dbb
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q969R5  (LMBL2_HUMAN) -  Lethal(3)malignant brain tumor-like protein 2 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		705 a.a.
392 a.a.
Protein chain
Pfam   ArchSchema ?
Q969R5  (LMBL2_HUMAN) -  Lethal(3)malignant brain tumor-like protein 2 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		705 a.a.
410 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
Nucleic Acids Res 37:2204-2210 (2009)
PubMed id: 19233876  
 
 
Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2.
Y.Guo, N.Nady, C.Qi, A.Allali-Hassani, H.Zhu, P.Pan, M.A.Adams-Cioaba, M.F.Amaya, A.Dong, M.Vedadi, M.Schapira, R.J.Read, C.H.Arrowsmith, J.Min.
 
  ABSTRACT  
 
The MBT repeat has been recently identified as a key domain capable of methyl-lysine histone recognition. Functional work has pointed to a role for MBT domain-containing proteins in transcriptional repression of developmental control genes such as Hox genes. In this study, L3MBTL2, a human homolog of Drosophila Sfmbt critical for Hox gene silencing, is demonstrated to preferentially recognize lower methylation states of several histone-derived peptides through its fourth MBT repeat. High-resolution crystallographic analysis of the four MBT repeats of this protein reveals its unique asymmetric rhomboid architecture, as well as binding mechanism, which preclude the interaction of the first three MBT repeats with methylated peptides. Structural elucidation of an L3MBTL2-H4K20me1 complex and comparison with other MBT-histone peptide complexes also suggests that an absence of distinct surface contours surrounding the methyl-lysine-binding pocket may underlie the lack of sequence specificity observed for members of this protein family.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23211769 C.A.Musselman, M.E.Lalonde, J.Côté, and T.G.Kutateladze (2012).
Perceiving the epigenetic landscape through histone readers.
  Nat Struct Mol Biol, 19, 1218-1227.  
21468892 C.Xu, and J.Min (2011).
Structure and function of WD40 domain proteins.
  Protein Cell, 2, 202-214.
PDB codes: 3e0c 3fm0 3i2n 3ow8
21252303 H.Honda, K.Takubo, H.Oda, K.Kosaki, T.Tazaki, N.Yamasaki, K.Miyazaki, K.A.Moore, Z.Honda, T.Suda, and I.R.Lemischka (2011).
Hemp, an mbt domain-containing protein, plays essential roles in hematopoietic stem cell function and skeletal formation.
  Proc Natl Acad Sci U S A, 108, 2468-2473.  
21245294 M.E.McLaughlin-Drubin, C.P.Crum, and K.Münger (2011).
Human papillomavirus E7 oncoprotein induces KDM6A and KDM6B histone demethylase expression and causes epigenetic reprogramming.
  Proc Natl Acad Sci U S A, 108, 2130-2135.  
21437264 N.Koester-Eiserfunke, and W.Fischle (2011).
H3K9me2/3 binding of the MBT domain protein LIN-61 is essential for Caenorhabditis elegans vulva development.
  PLoS Genet, 7, e1002017.  
21549307 S.P.Rowbotham, L.Barki, A.Neves-Costa, F.Santos, W.Dean, N.Hawkes, P.Choudhary, W.R.Will, J.Webster, D.Oxley, C.M.Green, P.Varga-Weisz, and J.E.Mermoud (2011).
Maintenance of Silent Chromatin through Replication Requires SWI/SNF-like Chromatin Remodeler SMARCAD1.
  Mol Cell, 42, 285-296.  
20923397 K.L.Yap, and M.M.Zhou (2010).
Keeping it in the family: diverse histone recognition by conserved structural folds.
  Crit Rev Biochem Mol Biol, 45, 488-505.  
20937909 K.Liu, C.Chen, Y.Guo, R.Lam, C.Bian, C.Xu, D.Y.Zhao, J.Jin, F.MacKenzie, T.Pawson, and J.Min (2010).
Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain.
  Proc Natl Acad Sci U S A, 107, 18398-18403.
PDB codes: 3omc 3omg
20698951 L.Addou-Klouche, J.Adélaïde, P.Finetti, N.Cervera, A.Ferrari, I.Bekhouche, F.Sircoulomb, C.Sotiriou, P.Viens, S.Moulessehoul, F.Bertucci, D.Birnbaum, and M.Chaffanet (2010).
Loss, mutation and deregulation of L3MBTL4 in breast cancers.
  Mol Cancer, 9, 213.  
20735237 L.Balakrishnan, and B.Milavetz (2010).
Decoding the histone H4 lysine 20 methylation mark.
  Crit Rev Biochem Mol Biol, 45, 440-452.  
21072162 M.A.Adams-Cioaba, Y.Guo, C.Bian, M.F.Amaya, R.Lam, G.A.Wasney, M.Vedadi, C.Xu, and J.Min (2010).
Structural studies of the tandem Tudor domains of fragile X mental retardation related proteins FXR1 and FXR2.
  PLoS One, 5, e13559.
PDB codes: 3h8z 3o8v
20466062 M.Vedadi, C.H.Arrowsmith, A.Allali-Hassani, G.Senisterra, and G.A.Wasney (2010).
Biophysical characterization of recombinant proteins: a key to higher structural genomics success.
  J Struct Biol, 172, 107-119.  
21124763 S.Pu, A.L.Turinsky, J.Vlasblom, T.On, X.Xiong, A.Emili, Z.Zhang, J.Greenblatt, J.Parkinson, and S.J.Wodak (2010).
Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human.
  PLoS One, 5, e14122.  
19841675 J.Eryilmaz, P.Pan, M.F.Amaya, A.Allali-Hassani, A.Dong, M.A.Adams-Cioaba, F.Mackenzie, M.Vedadi, and J.Min (2009).
Structural studies of a four-MBT repeat protein MBTD1.
  PLoS One, 4, e7274.
PDB code: 3feo
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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