Structure of PDB 4ffl Chain A

Receptor sequence

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

MKTICLVGGKLQGFEAAYLSKKAGMKVVLVDKNPQALIRNYADEFYCFDV
IKEPEKLLELSKRVDAVLPVNENLACIEFLNSIKEKFSCPVLFDFEAYRI
SRDKKKSKDYFKSIGVPTPQDRPSKPPYFVKPPCESSSVGARIIYGLEPD
TLVEEYVEGEVVSLEVVGDGSHFAVVKETLVHIDETYDCHMVTPLPANPL
FRQISHDLAANLPLKGIMDVEAIFGPKGLRVIEIDARFPSQTPTVVYYSS
GINLIELLFRAFTDGVEEIENKYCIYEHLMFGENGVLIPVGEQVLSMGSD
YGKFYEEPGIEIFLCKGEYPVFTMVFWGKDREETGAKRCKGLSVLKERFG
AVL

3D structure

• PDB: 4ffl Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution.
• Chain: A
• Resolution: 1.5 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	LYS	A	K10 L11 Q12 E72 S246 E302	K10 L11 Q12 E72 S240 E292
BS02	ADP	A	K104 F129 K131 S136 S138 Y162 V163 I229 I238 E239	K104 F129 K131 S136 S138 Y156 V157 I223 I232 E233
BS03	PO4	A	S137 E227 E239 D241 R243	S137 E221 E233 D235 R237
BS04	MG	A	E227 E239	E221 E233
BS05	MG	A	E239 D241	E233 D235
BS06	CO3	A	V187 E227 Q247	V181 E221 Q241
BS07	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:4ffl, PDBe:4ffl, PDBj:4ffl
• PDBsum: 4ffl
• PubMed: 22985965
• UniProt: Q46E79|PYLC_METBF 3-methyl-D-ornithine--L-lysine ligase (Gene Name=pylC)