Structure of PDB 4ffm Chain A

Receptor sequence

>4ffmA (length=344) Species: 269797 (Methanosarcina barkeri str. Fusaro)

MKTICLVGGKLQGFEAAYLSKKAGMKVVLVDKNPQALIRNYADEFYCFDV
IKEPEKLLELSKRVDAVLPVNENLACIEFLNSIKEKFSCPVLFDFEAYRI
SRDKKKSKDYFKSIGVPTPQDRPSKPPYFVKARIIYGLEPDTLVEEYVEG
EVVSLEVVGDGSHFAVVKETLVHIDETYDCHMVTPLPANPLFRQISHDLA
ANLPLKGIMDVEAIFGPKGLRVIEIDARFPSQTPTVVYYSSGINLIELLF
RAFTDGVEEIENKYCIYEHLMFGENGVLIPVGEQVLSMGSDYGKFYEEPG
IEIFLCKGEYPVFTMVFWGKDREETGAKRCKGLSVLKERFGAVL

3D structure

• PDB: 4ffm Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution.
• Chain: A
• Resolution: 1.91 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	0TF	A	K10 L11 Q12 E72 S169 D225 P245 S246 Q247 T248 E302	K10 L11 Q12 E72 S154 D210 P230 S231 Q232 T233 E283
BS02	ADP	A	K104 P119 F129 K131 E160 E161 Y162 V163 V167 E227 I229 E239	K104 P119 F129 K131 E145 E146 Y147 V148 V152 E212 I214 E224
BS03	MG	A	E227 E239	E212 E224
BS04	MG	A	E239 D241	E224 D226
BS05	ATP	A	K10 D31 K32 D49 I51 N71 N73 C76	K10 D31 K32 D49 I51 N71 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:4ffm, PDBe:4ffm, PDBj:4ffm
• PDBsum: 4ffm
• PubMed: 22985965
• UniProt: Q46E79|PYLC_METBF 3-methyl-D-ornithine--L-lysine ligase (Gene Name=pylC)