PDBsum entry: 3htx

Transferase/RNA

PDB id: 3htx

Contents

Protein chains

779 a.a. *

DNA/RNA

Ligands

SAH ×2

Metals

_MG ×2

Waters ×37

* Residue conservation analysis

PDB id:

3htx

Name:

Transferase/RNA

Title:

Crystal structure of small RNA methyltransferase hen1

Structure:

Hen1. Chain: a, d. Engineered: yes. Mutation: yes. 5'- r( Gp Ap Up Up Up Cp Up Cp Up Cp Up Gp Cp Ap Ap Gp Cp Gp Ap Ap Ap G)-3'. Chain: b, e. Engineered: yes.

Source:

Arabidopsis thaliana. Organism_taxid: 3702. Gene: hen1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes

Resolution:

3.10Å R-factor: 0.260 R-free: 0.288

Authors:

Y.Huang,L.-J.Ji,Q.-C.Huang,D.G.Vassylyev,X.-M.Chen,J.-B.Ma

Key ref:

Y.Huang et al. (2009). Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature, 461, 823-827. PubMed id: 19812675 DOI: 10.1038/nature08433

Date:

12-Jun-09 Release date: 29-Sep-09

Protein chains

Q9C5Q8  (HEN1_ARATH) -  Small RNA 2'-O-methyltransferase

Seq: 942 a.a.

Struc: 779 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.1.1 - Guanidinoacetate N-methyltransferase.
• Pathway: Creatine Biosynthesis
• Reaction: S-adenosyl-L-methionine + guanidinoacetate = S-adenosyl-L-homocysteine + creatine

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1038/nature08433

Nature 461:823-827 (2009)

PubMed id: 19812675

Structural insights into mechanisms of the small RNA methyltransferase HEN1.

Y.Huang, L.Ji, Q.Huang, D.G.Vassylyev, X.Chen, J.B.Ma.

ABSTRACT

RNA silencing is a conserved regulatory mechanism in fungi, plants and animals that regulates gene expression and defence against viruses and transgenes. Small silencing RNAs of approximately 20-30 nucleotides and their associated effector proteins, the Argonaute family proteins, are the central components in RNA silencing. A subset of small RNAs, such as microRNAs and small interfering RNAs (siRNAs) in plants, Piwi-interacting RNAs in animals and siRNAs in Drosophila, requires an additional crucial step for their maturation; that is, 2'-O-methylation on the 3' terminal nucleotide. A conserved S-adenosyl-l-methionine-dependent RNA methyltransferase, HUA ENHANCER 1 (HEN1), and its homologues are responsible for this specific modification. Here we report the 3.1 A crystal structure of full-length HEN1 from Arabidopsis in complex with a 22-nucleotide small RNA duplex and cofactor product S-adenosyl-l-homocysteine. Highly cooperative recognition of the small RNA substrate by multiple RNA binding domains and the methyltransferase domain in HEN1 measures the length of the RNA duplex and determines the substrate specificity. Metal ion coordination by both 2' and 3' hydroxyls on the 3'-terminal nucleotide and four invariant residues in the active site of the methyltransferase domain suggests a novel Mg(2+)-dependent 2'-O-methylation mechanism.

Selected figure(s)

Figure 1.
Figure 1: Structures of HEN1 in complex with a small RNA duplex and AdoHcy. a, Ribbon diagram of the complex. dsRBD, violet; La motif, chocolate; LCD, wheat; dsRDB2, cyan; PLD, purple; MTase, green; linkers including L1, L2 and L4, grey; RNA strand to be methylated (m strand), red; RNA strand not to be methylated (u strand), blue; AdoHcy, yellow; Mg^2+, brown. b, Ribbon diagram of the complex rotated by 90° about the horizontal axis relative to a. c, d, Surface and surface charge views of HEN1 in the complex in the same orientation as a. e, Schematic representation of the domains in HEN1 with the same colour codes as in a. The disordered L3 is represented by the dashed line. f, Sequences of the small RNA duplex used in the co-crystallization. The m strand and u strand are coloured red and blue, respectively, and the two termini, [5'-m:3'-u] and [5'-u:3'-m], are indicated.

Figure 3.
Figure 3: Small RNA substrate recognition by the MTase domain. a, The phosphate connecting the 2-nucleotide 3'-overhang of the m strand with the duplex region is specifically recognized by a conserved loop (F692–L697). The penultimate nucleotide A21[m] is flipped out and its base is stacked on the side chains of L835 and R856. The phosphate of the 2-nucleotide overhang is hydrogen bonded by R701 and R856. b, The base of the 3'-terminal nucleotide of the m strand G22[m] is stacked on the terminal base pair formed by A20[m] and U1[u] and the 5'-phosphate of the u strand is recognized by S747. c, Both 2' and 3' hydroxyls of the 3'-terminal nucleotide G22[m] are coordinated to Mg^2+ along with four invariant residues, E796, E799, H800 and H860. d, A stereo view of the Mg^2+ coordination covered with F[o ]- F[c] electron density omit map contoured at 3.0 .

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2009, 461, 823-827) copyright 2009.

Figures were selected by the author.