Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.38 kDa 
• Atom Count: 5000 
• Modelled Residue Count: 545 
• Deposited Residue Count: 603 
• Unique protein chains: 3

4I51

Methyltransferase domain of HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1, mutant Y1211A

• PDB DOI: 10.2210/pdb4I51/pdb
• Entry: 4I51 supersedes: 4H4H

• Classification: Transferase/Peptide
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-11-28 Released: 2012-12-19 
• Deposition Author(s): Dong, A., Zeng, H., Walker, J.R., Islam, K., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Lou, M., Min, J., Wu, H., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.195 
• R-Value Work: 0.171 
• R-Value Observed: 0.171 

Literature

Defining efficient enzyme-cofactor pairs for bioorthogonal profiling of protein methylation.

Islam, K., Chen, Y., Wu, H., Bothwell, I.R., Blum, G.J., Zeng, H., Dong, A., Zheng, W., Min, J., Deng, H., Luo, M.

(2013) Proc Natl Acad Sci U S A 110: 16778-16783

• PubMed: 24082136 
• DOI: 10.1073/pnas.1216365110
• Primary Citation of Related Structures:  
  4I51


• PubMed Abstract: 
  

Protein methyltransferase (PMT)-mediated posttranslational modification of histone and nonhistone substrates modulates stability, localization, and interacting partners of target proteins in diverse cellular contexts. These events play critical roles in normal biological processes and are frequently deregulated in human diseases. In the course of identifying substrates of individual PMTs, bioorthogonal profiling of protein methylation (BPPM) has demonstrated its merits. In this approach, specific PMTs are engineered to process S-adenosyl-L-methionine (SAM) analogs as cofactor surrogates and label their substrates with distinct chemical modifications for target elucidation. Despite the proof-of-concept advancement of BPPM, few efforts have been made to explore its generality. With two cancer-relevant PMTs, EuHMT1 (GLP1/KMT1D) and EuHMT2 (G9a/KMT1C), as models, we defined the key structural features of engineered PMTs and matched SAM analogs that can render the orthogonal enzyme-cofactor pairs for efficient catalysis. Here we have demonstrated that the presence of sulfonium-β-sp(2) carbon and flexible, medium-sized sulfonium-δ-substituents are crucial for SAM analogs as BPPM reagents. The bulky cofactors can be accommodated by tailoring the conserved Y1211/Y1154 residues and nearby hydrophobic cavities of EuHMT1/2. Profiling proteome-wide substrates with BPPM allowed identification of >500 targets of EuHMT1/2 with representative targets validated using native EuHMT1/2 and SAM. This finding indicates that EuHMT1/2 may regulate many cellular events previously unrecognized to be modulated by methylation. The present work, therefore, paves the way to a broader application of the BPPM technology to profile methylomes of diverse PMTs and elucidate their downstream functions.

---

Organizational Affiliation: 

Molecular Pharmacology and Chemistry Program and Tri-Institutional Training Program in Chemical Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase EHMT1	A, C [auth B]	286	Homo sapiens	Mutation(s): 1  Gene Names: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D EC: 2.1.1 (PDB Primary Data), 2.1.1.43 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9B1 (Homo sapiens) Explore Q9H9B1  Go to UniProtKB:  Q9H9B1
PHAROS:  Q9H9B1 GTEx:  ENSG00000181090

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3K9 NE-ALLYL PEPTIDE	B [auth C], D	9	Homo sapiens	Mutation(s): 0  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
UNKNOWN PEPTIDE	E [auth K]	13	N/A	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	F [auth A], U [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL	K [auth A], L [auth A], Z [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	G [auth A], H [auth A], I [auth A], J [auth A], V [auth B], W [auth B], X [auth B], Y [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	AA [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LDH	B [auth C], D	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Binding Affinity Annotations
ID	Source	Binding Affinity
SAH	BindingDB:  4I51	IC50: 230 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.195 
• R-Value Work: 0.171 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.497	α = 90
b = 83.8	β = 90
c = 95.052	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-28 
• Released Date: 2012-12-19 
Deposition Author(s): Dong, A., Zeng, H., Walker, J.R., Islam, K., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Lou, M., Min, J., Wu, H., Structural Genomics Consortium (SGC)
• This entry supersedes: 4H4H

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2013-12-04
  Changes: Database references
• Version 1.2: 2014-04-02
  Changes: Source and taxonomy