1LT8 | pdb_00001lt8

Deposited: 2002-05-20 Released: 2002-09-11
Deposition Author(s): Evans, J.C., Huddler, D.P., Jiracek, J., Castro, C., Millian, N.S., Garrow, T.A., Ludwig, M.L.

Experimental Data Snapshot

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

(2002) Structure 10: 1159-1171

PubMed Abstract:
Betaine-homocysteine methyl transferase (BHMT) catalyzes the synthesis of methionine from betaine and homocysteine (Hcy), utilizing a zinc ion to activate Hcy. BHMT is a key liver enzyme that is important for homocysteine homeostasis. X-ray structures of human BHMT in its oxidized (Zn-free) and reduced (Zn-replete) forms, the latter in complex with the bisubstrate analog, S(delta-carboxybutyl)-L-homocysteine, were determined at resolutions of 2.15 A and 2.05 A. BHMT is a (beta/alpha)(8) barrel that is distorted to construct the substrate and metal binding sites. The zinc binding sequences G-V/L-N-C and G-G-C-C are at the C termini of strands beta6 and beta8. Oxidation to the Cys217-Cys299 disulfide and expulsion of Zn are accompanied by local rearrangements. The structures identify Hcy binding fingerprints and provide a prototype for the homocysteine S-methyltransferase family.

Organizational Affiliation

Biophysics Research Division and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETAINE-HOMOCYSTEINE METHYLTRANSFERASE	A, B	406	Homo sapiens	Mutation(s): 6 EC: 2.1.1.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q93088 (Homo sapiens) Explore Q93088 Go to UniProtKB: Q93088
PHAROS: Q93088 GTEx: ENSG00000145692
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93088
Sequence Annotations Expand
Reference Sequence

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CBH Query on CBH Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	S-(D-CARBOXYBUTYL)-L-HOMOCYSTEINE C₉ H₁₇ N O₄ S BMONDXDFXRPNKQ-ZETCQYMHSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
CBH	BindingDB: 1LT8	Ki: 12 (nM) from 1 assay(s)
		Kd: 280 (nM) from 1 assay(s)
		IC50: min: 87, max: 138 (nM) from 3 assay(s)