Structure of PDB 8pu0 Chain C

Receptor sequence

>8pu0C (length=538) Species: 9606 (Homo sapiens) [Search protein sequence]

SPAELMMLTIGDVIKQLIEAHEQGKDIDLNKVKTKTAAKYGLSAQPRLVD
IIAAVPPQYRKVLMPKLKAKPIRTASGIAVVAVMCKPHRCPHISFTGNIC
VYCPGGPDSDFEYSTQSYTGYEPTSMRAIRARYDPFLQTRHRIEQLKQLG
HSVDKVEFIVMGGTFMALPEEYRDYFIRNLHDALSGHTSNNIYEAVKYSE
RSLTKCIGITIETRPDYCMKRHLSDMLTYGCTRLEIGVQSVYEDVARDTN
RGHTVKAVCESFHLAKDSGFKVVAHMMPDLPNVGLERDIEQFTEFFENPA
FRPDGLKLYPTLVIRGTGLYELWKSGRYKSYSPSDLVELVARILALVPPW
TRVYRVQRDIPMPLVSSGVEHGNLRELALARMKDLGIQCRDVRTREVGIQ
EIHHKVRPYQVELVRRDYVANGGWETFLSYEDPDQDILIGLLRLRKCSEE
TFRFELGGGVSIVRELHVYGSVVPVSSRDPTKFQHQGFGMLLMEEAERIA
REEHGSGKIAVISGVGTRNYYRKIGYRLQGPYMVKMLK

3D structure

PDB

8pu0 Cryo-EM structure of human Elp123 in complex with tRNA, desulpho-CoA, 5'-deoxyadenosine and methionine

Chain

Resolution

4.25 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

2.3.1.311: tRNA carboxymethyluridine 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)
BS01	rna	C	T43 A47 L51 S52 Q54 K79 I81 R82 Y127 E131 P132 T133 R136 R151 Q154 R361 R364 V365 D368 E379 N382 R384 E385	T34 A38 L42 S43 Q45 K70 I72 R73 Y118 E122 P123 T124 R127 R142 Q145 R352 R355 V356 D359 E370 N373 R375 E376
BS02	DCA	C	K164 K214 I216 V484 R487 Q493 H494 G496 G498 M499 T526 Y529 K532	K155 K205 I207 V475 R478 Q484 H485 G487 G489 M490 T517 Y520 K523
BS03	SF4	C	C99 H101 I108 C109 C112 Q125 S126 R260	C90 H92 I99 C100 C103 Q116 S117 R251
BS04	MET	C	E221 T222 R223 I245	E212 T213 R214 I236

Gene Ontology

	Molecular Function
GO:0000049	tRNA binding
GO:0003824	catalytic activity
GO:0005515	protein binding
GO:0008607	phosphorylase kinase regulator activity
GO:0016407	acetyltransferase activity
GO:0016746	acyltransferase activity
GO:0016747	acyltransferase activity, transferring groups other than amino-acyl groups
GO:0046872	metal ion binding
GO:0051536	iron-sulfur cluster binding
GO:0051539	4 iron, 4 sulfur cluster binding
GO:0106261	tRNA uridine(34) acetyltransferase activity

	Biological Process
GO:0001764	neuron migration
GO:0002098	tRNA wobble uridine modification
GO:0002926	tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation
GO:0006357	regulation of transcription by RNA polymerase II
GO:0006417	regulation of translation
GO:0007399	nervous system development
GO:0007417	central nervous system development
GO:0008033	tRNA processing
GO:0030335	positive regulation of cell migration

	Cellular Component
GO:0005634	nucleus
GO:0005730	nucleolus
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0033588	elongator holoenzyme complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:8pu0, PDBe:8pu0, PDBj:8pu0
PDBsum	8pu0
PubMed	38750017
UniProt	Q9H9T3\|ELP3_HUMAN Elongator complex protein 3 (Gene Name=ELP3)

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