1HMY

CRYSTAL STRUCTURE OF THE HHAI DNA METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYL-L-METHIONINE

PDB DOI: https://doi.org/10.2210/pdb1HMY/pdb

Classification: TRANSFERASE(METHYLTRANSFERASE)
Organism(s): Haemophilus haemolyticus
Mutation(s): No

Deposited: 1993-08-05 Released: 1993-10-31
Deposition Author(s): Cheng, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Work: 0.200
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine.

Cheng, X., Kumar, S., Posfai, J., Pflugrath, J.W., Roberts, R.J.

(1993) Cell 74: 299-307

PubMed: 8343957 Search on PubMed
DOI: https://doi.org/10.1016/0092-8674(93)90421-l
Primary Citation of Related Structures:
1HMY

PubMed Abstract:
The first three-dimensional structure of a DNA methyltransferase is presented. The crystal structure of the DNA (cytosine-5)-methyltransferase, M.HhaI (recognition sequence: GCGC), complexed with S-adenosyl-L-methionine has been determined and refined at 2.5 A resolution. The core of the structure is dominated by sequence motifs conserved among all DNA (cytosine-5)-methyltransferases, and these are responsible for cofactor binding and methyltransferase function.

Organizational Affiliation

W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, New York 11724.

Macromolecule Content

Total Structure Weight: 37.44 kDa
Atom Count: 2,633
Modelled Residue Count: 327
Deposited Residue Count: 327
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HaeIII METHYLTRANSFERASE	A	327	Haemophilus haemolyticus	Mutation(s): 0 EC: 2.1.1.37
UniProt
Find proteins for P05102 (Haemophilus parahaemolyticus) Explore P05102 Go to UniProtKB: P05102
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05102
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Work: 0.200
R-Value Observed: 0.200
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.3	α = 90
b = 72.7	β = 102.5
c = 91	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1993-10-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1993-10-31
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2012-02-01
Changes: Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.