PMID- 24678721
OWN - NLM
STAT- MEDLINE
DCOM- 20140609
LR  - 20211021
IS  - 1520-4995 (Electronic)
IS  - 0006-2960 (Print)
IS  - 0006-2960 (Linking)
VI  - 53
IP  - 15
DP  - 2014 Apr 22
TI  - 5-methylcytosine recognition by Arabidopsis thaliana DNA glycosylases DEMETER and 
      DML3.
PG  - 2525-32
LID - 10.1021/bi5002294 [doi]
AB  - Methylation of cytosine to 5-methylcytosine (5mC) is important for gene 
      expression, gene imprinting, X-chromosome inactivation, and transposon silencing. 
      Active demethylation in animals is believed to proceed by DNA glycosylase removal 
      of deaminated or oxidized 5mC. In plants, 5mC is removed from the genome directly 
      by the DEMETER (DME) family of DNA glycosylases. Arabidopsis thaliana DME excises 
      5mC to activate expression of maternally imprinted genes. Although the related 
      Repressor of Silencing 1 (ROS1) enzyme has been characterized, the molecular 
      basis for 5mC recognition by DME has not been investigated. Here, we present a 
      structure-function analysis of DME and the related DME-like 3 (DML3) glycosylases 
      for 5mC and its oxidized derivatives. Relative to 5mC, DME and DML3 exhibited 
      robust activity toward 5-hydroxymethylcytosine, limited activity for 
      5-carboxylcytosine, and no activity for 5-formylcytosine. We used homology 
      modeling and mutational analysis of base excision and DNA binding to identify 
      residues important for recognition of 5mC within the context of DNA and inside 
      the enzyme active site. Our results indicate that the 5mC binding pocket is 
      composed of residues from discrete domains and is responsible for discrimination 
      against 5mC derivatives, and suggest that DME, ROS1, and DML3 utilize subtly 
      different mechanisms to probe the DNA duplex for cytosine modifications.
FAU - Brooks, Sonja C
AU  - Brooks SC
AD  - Department of Biological Sciences and Center for Structural Biology, Vanderbilt 
      University , Nashville, Tennessee 37232, United States.
FAU - Fischer, Robert L
AU  - Fischer RL
FAU - Huh, Jin Hoe
AU  - Huh JH
FAU - Eichman, Brandt F
AU  - Eichman BF
LA  - eng
GR  - P30 ES000267/ES/NIEHS NIH HHS/United States
GR  - GM69415/GM/NIGMS NIH HHS/United States
GR  - R01 GM069415/GM/NIGMS NIH HHS/United States
GR  - P30 CA068485/CA/NCI NIH HHS/United States
GR  - T32 GM08320/GM/NIGMS NIH HHS/United States
GR  - ES019625/ES/NIEHS NIH HHS/United States
GR  - R01 ES019625/ES/NIEHS NIH HHS/United States
GR  - T32 GM008320/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20140409
PL  - United States
TA  - Biochemistry
JT  - Biochemistry
JID - 0370623
RN  - 0 (Arabidopsis Proteins)
RN  - 0 (DNA Primers)
RN  - 0 (Nuclear Proteins)
RN  - 0 (ROS1 protein, Arabidopsis)
RN  - 6R795CQT4H (5-Methylcytosine)
RN  - EC 3.2.2.- (DNA Glycosylases)
SB  - IM
MH  - 5-Methylcytosine/metabolism
MH  - Arabidopsis/*enzymology
MH  - Arabidopsis Proteins/metabolism
MH  - Base Sequence
MH  - DNA Glycosylases/chemistry/*metabolism
MH  - DNA Primers
MH  - Models, Molecular
MH  - Nuclear Proteins/metabolism
MH  - Polymerase Chain Reaction
MH  - Substrate Specificity
PMC - PMC4004242
EDAT- 2014/04/01 06:00
MHDA- 2014/06/10 06:00
PMCR- 2015/03/31
CRDT- 2014/04/01 06:00
PHST- 2014/04/01 06:00 [entrez]
PHST- 2014/04/01 06:00 [pubmed]
PHST- 2014/06/10 06:00 [medline]
PHST- 2015/03/31 00:00 [pmc-release]
AID - 10.1021/bi5002294 [doi]
PST - ppublish
SO  - Biochemistry. 2014 Apr 22;53(15):2525-32. doi: 10.1021/bi5002294. Epub 2014 Apr 
      9.