Structure of PDB 6opc Chain A

Receptor sequence

>6opcA (length=733) Species: 4932 (Saccharomyces cerevisiae)

KKDNMLLVDDAINDDNSVIAINSNTMDKLELFRGDTVLVKGKKRKDTVLI
VLIDDELEDGACRINRVVRNNLRIRLGDLVTIHPCPDIKYATRISVLPIA
DTIEGITGNLFDVFLKPYFVEAYRPVRKGDHFVVRGGMRQVEFKVVDVEP
EEYAVVAQDTIIHWEGEPINREDEENNMNEVGYDDIGGCRKQMAQIREMV
ELPLRHPQLFKAIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLIN
GPEVMSKMAGESESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEV
ERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIG
IPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAM
QQIREKMDLIDLDEDEIDAEVLDSLGVTMDNFRFALGNSNPSALRETVVE
SVNVTWDDVGGLDEIKEELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPP
GTGKTLLAKAVATEVSANFISVKGPELLSMWYGESESNIRDIFDKARAAA
PTVVFLDELDSIAKARGGDAGGASDRVVNQLLTEMDGMNAKKNVFVIGAT
NRPDQIDPAILRPGRLDQLIYVPLPDENARLSILNAQLRKTPLEPGLELT
AIAKATQGFSGADLLYIVQRAAKYAIKDSIEAHRQHEAEKEVEPEVDPVP
YITKEHFAEAMKTAKRSVSDAELRRYEAYSQQM

3D structure

• PDB: 6opc Structure of the Cdc48 segregase in the act of unfolding an authentic substrate.
• Chain: A
• Resolution: 3.7 Å

Enzymatic activity

• Enzyme Commision number: 3.6.4.6: vesicle-fusing ATPase.

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	peptide	A	M560 W561 Y562 A603	M530 W531 Y532 A570
BS02	ADP	A	G490 G531 T532 G533 K534 T535 L536 I666 Q670	G460 G501 T502 G503 K504 T505 L506 I633 Q637
BS03	BEF	A	P530 K534 N634	P500 K504 N601
BS04	ADP	A	G258 T259 G260 K261 T262 L263 H394 G418	G228 T229 G230 K231 T232 L233 H364 G388
BS05	BEF	A	P257 G258 K261	P227 G228 K231

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0019888 protein phosphatase regulator activity
• GO:0031593 polyubiquitin modification-dependent protein binding
• GO:0042802 identical protein binding
• GO:0043130 ubiquitin binding

Biological Process

• GO:0006274 DNA replication termination
• GO:0006515 protein quality control for misfolded or incompletely synthesized proteins
• GO:0010636 positive regulation of mitochondrial fusion
• GO:0015031 protein transport
• GO:0016236 macroautophagy
• GO:0016320 endoplasmic reticulum membrane fusion
• GO:0030970 retrograde protein transport, ER to cytosol
• GO:0031134 sister chromatid biorientation
• GO:0032984 protein-containing complex disassembly
• GO:0034517 ribophagy
• GO:0034727 piecemeal microautophagy of the nucleus
• GO:0036503 ERAD pathway
• GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
• GO:0043328 protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
• GO:0046034 ATP metabolic process
• GO:0051228 mitotic spindle disassembly
• GO:0070651 nonfunctional rRNA decay
• GO:0071629 cytoplasm protein quality control by the ubiquitin-proteasome system
• GO:0071630 nuclear protein quality control by the ubiquitin-proteasome system
• GO:0072344 rescue of stalled ribosome
• GO:0072671 mitochondria-associated ubiquitin-dependent protein catabolic process
• GO:0097352 autophagosome maturation
• GO:0099638 endosome to plasma membrane protein transport
• GO:0120174 stress-induced homeostatically regulated protein degradation pathway
• GO:1900182 positive regulation of protein localization to nucleus
• GO:1902979 mitotic DNA replication termination
• GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process
• GO:1990171 SCF complex disassembly in response to cadmium stress

Cellular Component

• GO:0000837 Doa10p ubiquitin ligase complex
• GO:0000839 Hrd1p ubiquitin ligase ERAD-L complex
• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005783 endoplasmic reticulum
• GO:0005789 endoplasmic reticulum membrane
• GO:0005829 cytosol
• GO:0030894 replisome
• GO:0034098 VCP-NPL4-UFD1 AAA ATPase complex
• GO:0036266 Cdc48p-Npl4p-Vms1p AAA ATPase complex
• GO:0043332 mating projection tip
• GO:1990112 RQC complex

External links

• PDB: RCSB:6opc, PDBe:6opc, PDBj:6opc
• PDBsum: 6opc
• PubMed: 31249134
• UniProt: P25694|CDC48_YEAST Cell division control protein 48 (Gene Name=CDC48)