Structure of PDB 6agg Chain Z

Receptor sequence

>6aggZ (length=420) Species: 224325 (Archaeoglobus fulgidus DSM 4304)

MRVWVGIDDTDSSRGMCTTYLAVLAMERVERELGKVIGFPRLIRLNPTIP
YKTRGNGAVSFLVEVDDVGELVDVVNEVIIEHAMLDDEKTNPGAVFVDEE
LAVKLKPFADKAIKDVLQIDEALFVIGKYFIPHLRHKKGRGLIGALAAVG
AELEDFTLELIAYRYPERFGTEREYDEESFFDMDYELYPQTFDNVDWCND
VVVCIPNTPCPVLYGIRGESVEALYKAMESVKTEPVDRRMIFVTNHATDM
HLIGEEEVHRLENYRSYRLRGRVTLEPYDIEGGHVFFEIDTKFGSVKCAA
FEPTKQFRNVIRLLRKGDVVEVYGSMKKDTINLEKIQIVELAEIWVEKNP
ICPSCGRRMESAGRGQGFRCKKCRTKADEKLREKVERELQPGFYEVPPSA
RRHLSKPLIRMNVEGRHIFR

3D structure

• PDB: 6agg Structure of tRNA-Modifying Enzyme TiaS and Motions of Its Substrate Binding Zinc Ribbon.
• Chain: Z
• Resolution: 2.706 Å

Enzymatic activity

• Enzyme Commision number: 6.3.4.22: tRNA(Ile)(2)-agmatinylcytidine synthase.

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	ACP	Z	D8 D9 D11 T18 L45 G55 N56 G57 A112 V116 L117 R140 G141 I143 G144	D8 D9 D11 T18 L45 G55 N56 G57 A112 V116 L117 R140 G141 I143 G144
BS02	AG2	Z	D193 N194 V203 C204 G215 R217	D193 N194 V203 C204 G215 R217	PDBbind-CN: -logKd/Ki=4.07,Kd=85uM
BS03	MG	Z	D9 D11 T18	D9 D11 T18
BS04	MG	Z	D8 T18 G57 A58	D8 T18 G57 A58

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0005524 ATP binding
• GO:0016874 ligase activity
• GO:0016879 ligase activity, forming carbon-nitrogen bonds

Biological Process

• GO:0002101 tRNA wobble cytosine modification
• GO:0008033 tRNA processing

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:6agg, PDBe:6agg, PDBj:6agg
• PDBsum: 6agg
• PubMed: 30121296
• UniProt: O28025|TIAS_ARCFU tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS (Gene Name=tiaS)