Structure of PDB 6o82 Chain A

Receptor sequence

>6o82A (length=986) Species: 284812 (Schizosaccharomyces pombe 972h-)

TIDEGLYSRQLYVLGHEAMKQMSQSNVLIIGCKGLGVEIAKNVCLAGVKS
VTLYDPQPTRIEDLSSQYFLTEDDIGVPRAKVTVSKLAELNQYVPVSVVD
ELSTEYLKNFKCVVVTETSLTKQLEINDFTHKNHIAYIAADSRGLFGSIF
CDFGENFICTDTDGNEPLTGMIASITDDGVVTMLEETRHGLENGDFVKFT
EVKGMPGLNDGTPRKVEVKGPYTFSIGSVKDLGSAGYNGVFTQVKVPTKI
SFKSLRESLKDPEYVYPDFGKMMRPPQYHIAFQALSAFADAHEGSLPRPR
NDIDAAEFFEFCKKIASTLQFDVELDEKLIKEISYQARGDLVAMSAFLGG
AVAQEVLKATTSKFYPLKQYFYFDSLESLPSSVTISEETCKPRGCRYDGQ
IAVFGSEFQEKIASLSTFLVGAGAIGCEMLKNWAMMGVATGESGHISVTD
MDSIEKSNLNRQFLFRPRDVGKLKSECASTAVSIMNPSLTGKITSYQERV
GPESEGIFGDEFFEKLSLVTNALDNVEARMYVDRRCVFFEKPLLESGTLG
TKGNTQVVVPHLTESYGSSQDPPEKSFPICTLKNFPNRIEHTIAWARDLF
EGLFKQPIDNVNMYLSSPNFLETSLKTSSNPREVLENIRDYLVTEKPLSF
EECIMWARLQFDKFFNNNIQQLLFNFPKDSVTSTGQPFWSGPKRAPTPLS
FDIHNREHFDFIVAAASLYAFNYGLKSETDPAIYERVLAGYNPPPFAPKS
GIKIQVDKQELKSIADSLPPPSSLVGFRLTPAEFEKDDDSNHHIDFITAA
SNLRAMNYDITPADRFKTKFVAGKIVPAMCTSTAVVSGLVCLELVKLVDG
KKKIEEYKNGFFNLAIGLFTFSDPIASPKMKVNGKEIDKIWDRYNLPDCT
LQELIDYFQKEEGLEVTMLSSGVSLLYANFQPPKKLAERLPLKISELVEQ
ITKKKLEPFRKHLVLEICCDDANGEDVEVPFICIKL

3D structure

• PDB: 6o82 Structural basis for adenylation and thioester bond formation in the ubiquitin E1.
• Chain: A
• Resolution: 2.604 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): R22 R474 D537 C593 T594 K596
• Catalytic site (residue number reindexed from 1): R9 R461 D524 C580 T581 K583
• Enzyme Commision number: 6.2.1.45: E1 ubiquitin-activating enzyme.

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	POP	A	R22 N471 R474 K487	R9 N458 R461 K474
BS02	POP	A	G28 H29 E30	G15 H16 E17
BS03	JZU	A	A437 D463 M464 K487 R512 V513 A535 L536 D537 N538	A424 D450 M451 K474 R499 V500 A522 L523 D524 N525

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0004839 ubiquitin activating enzyme activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008641 ubiquitin-like modifier activating enzyme activity
• GO:0016874 ligase activity
• GO:0016887 ATP hydrolysis activity

Biological Process

• GO:0006511 ubiquitin-dependent protein catabolic process
• GO:0006974 DNA damage response
• GO:0016567 protein ubiquitination
• GO:0036211 protein modification process

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:6o82, PDBe:6o82, PDBj:6o82
• PDBsum: 6o82
• PubMed: 31235585
• UniProt: O94609|UBA1_SCHPO Ubiquitin-activating enzyme E1 1 (Gene Name=ptr3)