Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger.
Human L3MBTL1, which contains three malignant brain tumor (MBT) repeats, binds monomethylated and dimethylated lysines, but not trimethylated lysines, in several histone sequence contexts. In crystal structures of L3MBTL1 complexes, the monomethyl- and dimethyllysines insert into a narrow and deep cavity of aromatic residue-lined pocket 2, while a proline ring inserts into shallower pocket 1. We have also engineered a single Y to E substitution within the aromatic cage of the BPTF PHD finger, resulting in a reversal of binding preference from trimethyl- to dimethyllysine in an H3K4 sequence context. In both the "cavity insertion" (L3MBTL1) and "surface groove" (PHD finger) modes of methyllysine recognition, a carboxylate group both hydrogen bonds and ion pairs to the methylammonium proton. Our structural and binding studies of these two modules provide insights into the molecular principles governing the decoding of lysine methylation states, thereby highlighting a methylation state-specific layer of histone mark readout impacting on epigenetic regulation.
Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
Haitao
H
Li
Wolfgang
W
Fischle
Wooikoon
W
Wang
Elizabeth M
EM
Duncan
Lena
L
Liang
Satoko
S
Murakami-Ishibe
C David
CD
Allis
Dinshaw J
DJ
Patel
D000595:Amino Acid Sequence; D034961:Antigens, Nuclear / Q000378:metabolism; D002868:Chromosomal Proteins, Non-Histone; D018360:Crystallography, X-Ray; D004252:DNA Mutational Analysis; D018698:Glutamic Acid / Q000235:genetics; D006657:Histones / Q000378:metabolism; D006801:Humans; D007700:Kinetics; D008239:Lysine / Q000378:metabolism*; D008745:Methylation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D050505:Mutant Proteins / Q000378:metabolism; D009363:Neoplasm Proteins / Q000737:chemistry* / Q000378:metabolism*; D009419:Nerve Tissue Proteins / Q000378:metabolism; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D015202:Protein Engineering / Q000379:methods*; D017434:Protein Structure, Tertiary; D020449:Repetitive Sequences, Amino Acid; D012097:Repressor Proteins; D013329:Structure-Activity Relationship; D014157:Transcription Factors / Q000378:metabolism; D025521:Tumor Suppressor Proteins; D014443:Tyrosine / Q000235:genetics; D000092468:Bromodomain Containing Proteins
D034961:Antigens, Nuclear; D002868:Chromosomal Proteins, Non-Histone; D018698:Glutamic Acid; D006657:Histones; D008239:Lysine; D050505:Mutant Proteins; D009363:Neoplasm Proteins; D009419:Nerve Tissue Proteins; D010455:Peptides; D012097:Repressor Proteins; D014157:Transcription Factors; D025521:Tumor Suppressor Proteins; D014443:Tyrosine; C120887:L3MBTL1 protein, human; C406238:fetal Alzheimer antigen; D000092468:Bromodomain Containing Proteins