Structure of PDB 8dav Chain D

Receptor sequence

>8davD (length=547) Species: 4932 (Saccharomyces cerevisiae)

GKKRKDVVRNNLRENNMNEVGYDDIGGCRKQMAQIREMVELPLRHPQLFK
AIGIKPPRGVLMYGPPGTGKTLMARAVANETGAFFFLINGPEVMSKMAGE
SESNLRKAFEEAEKNAPAIIFIDEIDSIAPKRDKTNGEVERRVVSQLLTL
MDGMKARSNVVVIAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEVL
RIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEAAMQQIREKMDLII
DAEVLDSLGVTMDNFRFALGNSNPSALRETVVESVNVTWDDVGGLDEIKE
ELKETVEYPVLHPDQYTKFGLSPSKGVLFYGPPGTGKTLLAKAVATEVSA
NFISVKGPELLSMWYGESESNIRDIFDKARAAAPTVVFLDELDSIASDRV
VNQLLTEMDGMNAKKNVFVIGATNRPDQIDPAILRPGRLDQLIYVPLPDE
NARLSILNAQLRKTPLEPGLELTAIAKATQGFSGADLLYIVQRAAKYAIK
DSIEAHRQDPVPYITKEHFAEAMKTAKRSVSDAELRRYEAYSQQMKA

3D structure

• PDB: 8dav SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex.
• Chain: D
• Resolution: 3.5 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	ATP	D	I216 G258 T259 G260 K261 T262 H394 G418	I25 G67 T68 G69 K70 T71 H203 G227
BS02	ADP	D	G490 P530 G531 T532 G533 K534 T535 I666	G293 P333 G334 T335 G336 K337 T338 I456

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:8dav, PDBe:8dav, PDBj:8dav
• PDBsum: 8dav
• PubMed: 36574706
• UniProt: P25694|CDC48_YEAST Cell division control protein 48 (Gene Name=CDC48)