PDBsum entry 2w5y

Transferase

PDB id: 2w5y

Contents

Protein chain

170 a.a. *

Ligands

SAH

Metals

_ZN

Waters ×130

* Residue conservation analysis

PDB id:

2w5y

Name:

Transferase

Title:

Binary complex of the mixed lineage leukaemia (mll1) set domain with the cofactor product s-adenosylhomocysteine.

Structure:

Histone-lysine n-methyltransferase hrx. Chain: a. Fragment: methyltransferase domain, residues 3785-3969. Synonym: zinc finger protein hrx, all-1, trithorax-like protein, lysine n-methyltransferase 2a, cxxc-type zinc finger protein 7, mll- 1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: rosetta 2.

Resolution:

2.00Å R-factor: 0.191 R-free: 0.264

Authors:

S.M.Southall,P.S.Wong,Z.Odho,S.M.Roe,J.R.Wilson

Key ref:

S.M.Southall et al. (2009). Structural basis for the requirement of additional factors for MLL1 SET domain activity and recognition of epigenetic marks. Mol Cell, 33, 181-191. PubMed id: 19187761 DOI: 10.1016/j.molcel.2008.12.029

Date:

15-Dec-08 Release date: 10-Feb-09

Protein chain

Q03164  (KMT2A_HUMAN) -  Histone-lysine N-methyltransferase 2A from Homo sapiens

Seq: 3969 a.a.

Struc: 170 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.1.1.- - ?????
• Enzyme class 2: E.C.2.1.1.364 - [histone H3]-lysine(4) N-methyltransferase.
• Reaction: L-lysyl₄-[histone H3] + S-adenosyl-L-methionine = N₆-methyl-L- lysyl₄-[histone H3] + S-adenosyl-L-homocysteine + H⁺

L-lysyl(4)-[histone H3] + S-adenosyl-L-methionine = N(6)-methyl-L- lysyl(4)-[histone H3] + S-adenosyl-L-homocysteine (Bound ligand (Het Group name = SAH) corresponds exactly) + H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

DOI no: 10.1016/j.molcel.2008.12.029

Mol Cell 33:181-191 (2009)

PubMed id: 19187761

Structural basis for the requirement of additional factors for MLL1 SET domain activity and recognition of epigenetic marks.

S.M.Southall, P.S.Wong, Z.Odho, S.M.Roe, J.R.Wilson.

ABSTRACT

The mixed-lineage leukemia protein MLL1 is a transcriptional regulator with an essential role in early development and hematopoiesis. The biological function of MLL1 is mediated by the histone H3K4 methyltransferase activity of the carboxyl-terminal SET domain. We have determined the crystal structure of the MLL1 SET domain in complex with cofactor product AdoHcy and a histone H3 peptide. This structure indicates that, in order to form a well-ordered active site, a highly variable but essential component of the SET domain must be repositioned. To test this idea, we compared the effect of the addition of MLL complex members on methyltransferase activity and show that both RbBP5 and Ash2L but not Wdr5 stimulate activity. Additionally, we have determined the effect of posttranslational modifications on histone H3 residues downstream and upstream from the target lysine and provide a structural explanation for why H3T3 phosphorylation and H3K9 acetylation regulate activity.

Selected figure(s)

Figure 1.
Figure 1. Overall Structure of the MLL1 SET Domain
(A) Schematic representation of the full-length MLL1 protein and the construct containing the SET domain used in structural studies (residues 3785–3969), indicating the subdomains referred to in the text. The N-flanking region is in pale blue, the SET-N in pale green, the SET-I in blue, the SET-C in bright green, and the postSET domain in orange.
(B) Sequence of the MLL1 SET domain aligned with MLL1, Dim-5, Suv39h2, Set7/9, and PRSet7. The SET domain region secondary structure elements derived from the structure are indicated above the sequence. Identical residues are highlighted in red, conserved cysteines involved in Zn binding in orange, and active site residues in blue.
(C) Two views of a cartoon representation of the MLL1 SET domain structure with a stick representation of the cofactor product AdoHcy (gray) and histone peptide substrate (purple).

Figure 3.
Figure 3. Ordering of the MLL1 Active Site
(A) Overlay of the SET-I region and C-flanking region of MLL1 (gray), and Dim-5 (yellow, PDB; 1PEG). Structures are superposed on their cofactors and overlap on their C-flanking domains.
(B) Superposition of active site residues in the SET domains of MLL1 and Dim-5 showing the displacement of the channel tetrapeptide in MLL1.
(C) Reorientation of SET-I; surface representation of the MLL1 ternary complex on the left showing open configuration of the active site. On the right, the MLL1 Set-I domain (green) has been modeled to align with the position observed in Dim5.
(D) Schematic representation of the MLL1 complex.
(E) Methyltransferase activity of MLL1 in the presence of Ash2L-Dpy30 heterodimer Wdr5-RbBP5 heterodimer, Wdr5, RbBP5, and Ash2L-DPY30 + Wdr5-RbBP5. Activity is represented as the mean of triplicate measurements, with error bars indicating one standard deviation.

The above figures are reprinted by permission from Cell Press: Mol Cell (2009, 33, 181-191) copyright 2009.

Figures were selected by the author.