Structure of PDB 6o83 Chain A

Receptor sequence

>6o83A (length=954) Species: 284812 (Schizosaccharomyces pombe 972h-)

SNVLIIGCKGLGVEIAKNVCLAGVKSVTLYDPQPTRIEDLSSQYFLTEDD
IGVPRAKVTVSKLAELNQYVPVSVVDELSTEYLKNFKCVVVTETSLTKQL
EINDFTHKNHIAYIAADSRGLFGSIFCDFGENFICTDTDGNEPLTGMIAS
ITDDGVVTMLEETRHGLENGDFVKFTEVKGMPGLNDGTPRKVEVKGPYTF
SIGSVKDLGSAGYNGVFTQVKVPTKISFKSLRESLKDPEYVYPDFGKMMR
PPQYHIAFQALSAFADAHEGSLPRPRNDIDAAEFFEFCKKIASTLQFDVE
LDEKLIKEISYQARGDLVAMSAFLGGAVAQEVLKATTSKFYPLKQYFYFD
SLESLPSSVTISEETCKPRGCRYDGQIAVFGSEFQEKIASLSTFLVGAGA
IGCEMLKNWAMMGVATGESGHISVTDMDSIEKSNLNRQFLFRPRDVGKLK
SECASTAVSIMNPSLTGKITSYQERVGPESEGIFGDEFFEKLSLVTNALD
NVEARMYVDRRCVFFEKPLLESGTLGTKGNTQVVVPHLTESYGSSQDPPE
KSFPICTLKNFPNRIEHTIAWARDLFEGLFKQPIDNVNMYLSSPNFLETS
LKTSSNPREVLENIRDYLVTEKPLSFEECIMWARLQFDKFFNNNIQQLLF
NFPKDSVTSTGQPFWSGPKRAPTPLSFDIHNREHFDFIVAAASLYAFNYG
LKSETDPAIYERVLAGYNPPPFAPDKQELKSIADSLPPPSSLVGFRLTPA
EFEKDDDSNHHIDFITAASNLRAMNYDITPADRFKTKFVAGKIVPAMCTS
TAVVSGLVCLELVKLVDGKKKIEEYKNGFFNLAIGLFTFSDPIASPKMKV
NGKEIDKIWDRYNLPDCTLQELIDYFQKEEGLEVTMLSSGVSLLYANFQP
PKKLAERLPLKISELVEQITKKKLEPFRKHLVLEICCDDANGEDVEVPFI
CIKL

3D structure

• PDB: 6o83 Structural basis for adenylation and thioester bond formation in the ubiquitin E1.
• Chain: A
• Resolution: 3.153 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): R474 D537 C593 T594 K596
• Catalytic site (residue number reindexed from 1): R437 D500 C556 T557 K559
• 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	CA	A	H305 E320	H268 E283
BS02	VMX	A	I438 D463 M464 D465 K487 V513 A535 D537 N538 T561 C593	I401 D426 M427 D428 K450 V476 A498 D500 N501 T524 C556

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:6o83, PDBe:6o83, PDBj:6o83
• PDBsum: 6o83
• PubMed: 31235585
• UniProt: O94609|UBA1_SCHPO Ubiquitin-activating enzyme E1 1 (Gene Name=ptr3)