Structure of PDB 4ffo Chain A

Receptor sequence

>4ffoA (length=353) Species: 269797 (Methanosarcina barkeri str. Fusaro)

MKTICLVGGKLQGFEAAYLSKKAGMKVVLVDKNPQALIRNYADEFYCFDV
IKEPEKLLELSKRVDAVLPVNENLACIEFLNSIKEKFSCPVLFDFEAYRI
SRDKKKSKDYFKSIGVPTPQDRPSKPPYFVKPPCESSSVGARIIYGLEPD
TLVEEYVEGEVVSLEVVGDGSHFAVVKETLVHIDETYDCHMVTPLPANPL
FRQISHDLAANLPLKGIMDVEAIFGPKGLRVIEIDARFPSQTPTVVYYSS
GINLIELLFRAFTDGVEEIENKYCIYEHLMFGENGVLIPVGEQVLSMGSD
YGKFYEEPGIEIFLCKGEYPVFTMVFWGKDREETGAKRCKGLSVLKERFG
AVL

3D structure

• PDB: 4ffo Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution.
• Chain: A
• Resolution: 2.0 Å

Enzymatic activity

• Enzyme Commision number: 6.3.2.59: 3-methyl-D-ornithine--L-lysine ligase.

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	0TK	A	S137 S169 D225 E227 E239 D241 R243 S246 T248 E302	S137 S163 D219 E221 E233 D235 R237 S240 T242 E292
BS02	ADP	A	K104 F129 K131 S136 S138 Y162 V163 E227 I229 I238 E239	K104 F129 K131 S136 S138 Y156 V157 E221 I223 I232 E233
BS03	MG	A	E227 E239	E221 E233
BS04	MG	A	E239 D241	E233 D235
BS05	ATP	A	G8 K10 D31 K32 D49 V50 I51 N71 E72 N73 C76	G8 K10 D31 K32 D49 V50 I51 N71 E72 N73 C76

Gene Ontology

Molecular Function

• GO:0005524 ATP binding
• GO:0016874 ligase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0008652 amino acid biosynthetic process
• GO:0071524 pyrrolysine biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:4ffo, PDBe:4ffo, PDBj:4ffo
• PDBsum: 4ffo
• PubMed: 22985965
• UniProt: Q46E79|PYLC_METBF 3-methyl-D-ornithine--L-lysine ligase (Gene Name=pylC)