2F4M | pdb_00002f4m

The Mouse PNGase-HR23 Complex Reveals a Complete Remodulation of the Protein-Protein Interface Compared to its Yeast Orthologs

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2f4mb2	All alpha proteins	XPC-binding domain-like	XPC-binding domain	XPC-binding domain	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d2f4mb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d2f4ma1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Transglutaminase core	Peptide:N-glycanase 1, PNG1	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d2f4ma2	Artifacts	Tags	Tags	Tags	C-terminal Tags	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	XPC-binding domain	8028192	4000673	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	XPC-binding domain	8040571	3000974	SCOP2 (2022-06-29)
A	SCOP2 Family	Transglutaminase core	8020479	4000877	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cysteine proteinases	8032859	3001808	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	XPC-binding	e2f4mB1	A: alpha arrays	X: HTH	H: XPC-binding domain (From Topology)	T: XPC-binding domain	F: XPC-binding	ECOD (1.6)
A	Transglut_core	e2f4mA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Transglut_core	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.10.540	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	XPC-binding domain	CATH (4.3.0)
A	3.10.620.30	Alpha Beta	Roll	C8orf32 fold		CATH (4.3.0)
A	2.20.25.10	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF09280	XPC-binding domain (XPC-binding)	XPC-binding domain	Members of this family adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair [1].	Domain
A	PF01841	Transglutaminase-like superfamily (Transglut_core)	Transglutaminase-like superfamily	This domain is found in animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that ...	This domain is found in animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterised transglutaminase, the human blood clotting factor XIIIa' [1]. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase [2], it is proposed that many, if not all, microbial homologues of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease. [3]	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	UV excision repair protein RAD23 homolog B	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding damaged DNA binding polyubiquitin modification-dependent protein binding modification-dependent protein binding DNA damage sensor activity molecular sensor activity molecular function regulator activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation catabolic process proteolysis involved in protein catabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process macromolecule metabolic process protein metabolic process multicellular organism development multicellular organismal process anatomical structure development animal organ development embryonic organ development embryo development regulation of cellular process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process regulation of proteolysis involved in protein catabolic process regulation of proteolysis regulation of biological process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of proteasomal protein catabolic process regulation of metabolic process regulation of protein catabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleotide-excision repair DNA repair response to peptide response to interleukin-7 response to chemical response to cytokine cellular response to cytokine stimulus cellular response to interleukin-7	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex catalytic complex peptidase complex proteasome complex endopeptidase complex intracellular protein-containing complex XPC complex nuclear protein-containing complex nucleotide-excision repair complex
A	peptide N-glycanase	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity hydrolase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding ion binding binding metal ion binding small molecule binding	carbohydrate derivative catabolic process glycoprotein catabolic process catabolic process carbohydrate derivative metabolic process primary metabolic process protein catabolic process glycoprotein metabolic process macromolecule catabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR004806	UV excision repair protein Rad23	Family
B	IPR036353	XPC-binding domain superfamily	Homologous Superfamily
B	IPR015360	XPC-binding domain	Domain
B	IPR015940	Ubiquitin-associated domain	Domain
B	IPR041811	RAD23A/RAD23B, UBA1 domain	Domain
B	IPR000626	Ubiquitin-like domain	Domain
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
B	IPR009060	UBA-like superfamily	Homologous Superfamily
B	IPR006636	Heat shock chaperonin-binding	Domain
A	IPR036339	PUB-like domain superfamily	Homologous Superfamily
A	IPR018997	PUB domain	Domain
A	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A	IPR050883	Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase	Family
A	IPR038680	PAW domain superfamily	Homologous Superfamily
A	IPR002931	Transglutaminase-like	Domain
A	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A	IPR006588	Peptide N glycanase, PAW domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.