Structure of PDB 4ffn Chain A

Receptor sequence

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

MKTICLVGGKLQGFEAAYLSKKAGMKVVLVDKNPQALIRNYADEFYCFDV
IKEPEKLLELSKRVDAVLPVNENLACIEFLNSIKEKFSCPVLFDFEAYRI
SRDKKKSKDYFKSIGVPTPQDRPSKPPYFVKPPCESSSVGARIIYGLEPD
TLVEEYVEGEVVSLEVVGDGSHFAVVKETLVHIDETYDCHMVTPLPANPL
FRQISHDLAANLPLKGIMDVEAIFGPKGLRVIEIDARFPSQTPTVVYYSS
GINLIELLFRAFTDGVEEIENKYCIYEHLMFGENGVLIPVGEQVLSMGSD
YGKFYEEPGIEIFLCKGEYPVFTMVFWGKDREETGAKRCKGLSVLKERFG
AVL

3D structure

• PDB: 4ffn Biosynthesis of the 22nd genetically encoded amino acid pyrrolysine: structure and reaction mechanism of PylC at 1.5A resolution.
• Chain: A
• Resolution: 2.4 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	ORD	A	S169 D225 R243 S246 Q247 T248 E302	S163 D219 R237 S240 Q241 T242 E292
BS02	ANP	A	K104 F129 K131 E135 S136 S137 S138 Y162 V163 V167 I189 Y193 E227 I229 I238 E239 D241	K104 F129 K131 E135 S136 S137 S138 Y156 V157 V161 I183 Y187 E221 I223 I232 E233 D235
BS03	MG	A	E227 E239	E221 E233
BS04	MG	A	E239 D241	E233 D235
BS05	ATP	A	G8 K10 D31 K32 D49 N71 E72 N73 C76	G8 K10 D31 K32 D49 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:4ffn, PDBe:4ffn, PDBj:4ffn
• PDBsum: 4ffn
• PubMed: 22985965
• UniProt: Q46E79|PYLC_METBF 3-methyl-D-ornithine--L-lysine ligase (Gene Name=pylC)