Structure of PDB 6vcy Chain A

Receptor sequence

>6vcyA (length=385) Species: 3702 (Arabidopsis thaliana)

METFLFTSESVNEGHPDKLCDQISDAVLDACLEQDPDSKVACETCTKTNM
VMVFGEITTKATVDYEKIVRDTCRAIGFVSDDVGLDADKCKVLVNIEQQS
PDIAQGVKCPEEIGAGDQGHMFGYATDETPELMPLSHVLATKLGARLTEV
RKNGTCAWLRPDGKTQVTVEYYNDKGAMVPIRVHTVLISTQHDETVTNDE
IARDLKEHVIKPVIPEKYLDEKTIFHLNPSGRFVIGGPHGDAGLTGRKII
IDTYGGWGAHGGGAFSGKDPTKVDRSGAYIVRQAAKSVVANGMARRALVQ
VSYAIGVPEPLSVFVDTYETGLIPDKEILKIVKESFDFRPGMMTINLDLK
RGGNGRFLKTAAYGHFGRDDPDFTWEVVKPLKWDK

3D structure

• PDB: 6vcy S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula.
• Chain: A
• Resolution: 1.82 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H15 D17 K18 E43 E56 K169 F238 D246 A247 R252 K253 K273 K277 D279
• Catalytic site (residue number reindexed from 1): H15 D17 K18 E43 E56 K164 F233 D241 A242 R247 K248 K268 K272 D274
• Enzyme Commision number: 2.5.1.6: methionine adenosyltransferase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	MTA	A	H15 D167 S235 F238 D246	H15 D162 S230 F233 D241

Gene Ontology

Molecular Function

• GO:0004478 methionine adenosyltransferase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016740 transferase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006556 S-adenosylmethionine biosynthetic process
• GO:0006730 one-carbon metabolic process
• GO:0009693 ethylene biosynthetic process

Cellular Component

• GO:0005576 extracellular region
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0009505 plant-type cell wall

External links

• PDB: RCSB:6vcy, PDBe:6vcy, PDBj:6vcy
• PDBsum: 6vcy
• PubMed: 32057875
• UniProt: P23686|METK1_ARATH S-adenosylmethionine synthase 1 (Gene Name=SAM1)