Structure of PDB 4ffr Chain A

Receptor sequence

>4ffrA (length=347) Species: 269797 (Methanosarcina barkeri str. Fusaro)

MKTICLVGGKLQGFEAAYLSKKAGMKVVLVDKNPQALIRNYADEFYCFDV
IKEPEKLLELSKRVDAVLPVNENLACIEFLNSIKEKFSCPVLFDFEAYRI
SRDKKKSKDYFKSIGVPTPQDRPSKPPYFVKPPCESSSVGARIIYDDKDE
PDTLVEEYVEGEVVSLEVVGDGSHFAVVKETLVHIDETYDCHMVTPLPAN
PLFRQISHDLAANLPLKGIMDVEAIFGPKGLRVIEIDARFPSQTPTVVYY
SSGINLIELLFRAFTDGVEEIENKYCIYEHLMFGENGVLIPVGEQVLSMG
SDYGKFYEEPGIEIFLCKGEYPVFTMVFWGKDREETGAKRCKGLSVL

3D structure

• PDB: 4ffr Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution.
• Chain: A
• Resolution: 1.8 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	ATP	A	K104 F129 K131 S136 S137 S138 Y162 V163 E227 I229 E239 D241	K104 F129 K131 S136 S137 S138 Y158 V159 E223 I225 E235 D237
BS02	ATP	A	G8 K10 D31 K32 D49 V50 I51 N71 E72 N73 C76	G8 K10 D31 K32 D49 V50 I51 N71 E72 N73 C76
BS03	MG	A	E227 E239	E223 E235
BS04	MG	A	E239 D241	E235 D237
BS05	MG	A	S169 L170 E171 T185	S165 L166 E167 T181
BS06	MG	A	S101 E239 I240 D241	S101 E235 I236 D237

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