3OQ0 | pdb_00003oq0

Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J	Beta_elim_lyase	e3oq0J1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Class I glutamine amidotransferase-like	F: Beta_elim_lyase	ECOD (v295.2)
I	Beta_elim_lyase	e3oq0I1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Class I glutamine amidotransferase-like	F: Beta_elim_lyase	ECOD (v295.2)
H	Beta_elim_lyase	e3oq0H1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Class I glutamine amidotransferase-like	F: Beta_elim_lyase	ECOD (v295.2)
G	Beta_elim_lyase	e3oq0G1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Class I glutamine amidotransferase-like	F: Beta_elim_lyase	ECOD (v295.2)
F	Beta_elim_lyase	e3oq0F1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Class I glutamine amidotransferase-like	F: Beta_elim_lyase	ECOD (v295.2)
E	Beta_elim_lyase	e3oq0E1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Class I glutamine amidotransferase-like	F: Beta_elim_lyase	ECOD (v295.2)
D	Beta_elim_lyase	e3oq0D1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Class I glutamine amidotransferase-like	F: Beta_elim_lyase	ECOD (v295.2)
C	Beta_elim_lyase	e3oq0C1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Class I glutamine amidotransferase-like	F: Beta_elim_lyase	ECOD (v295.2)
B	Beta_elim_lyase	e3oq0B1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Class I glutamine amidotransferase-like	F: Beta_elim_lyase	ECOD (v295.2)
A	Beta_elim_lyase	e3oq0A1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Class I glutamine amidotransferase-like	F: Beta_elim_lyase	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	3.40.50.10190	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	BRCT domain	CATH (4.3.0)
G	3.40.50.10190	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	BRCT domain	CATH (4.3.0)
B	3.40.50.10190	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	BRCT domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	PF22437	BRCT domain (DBF4_BRCT)	BRCT domain	This entry represents the BRCT domain found in Dbf4 protein. Dbf4 is a conserved eukaryotic protein that functions as the regulatory subunit of the Dbf4-dependent kinase (DDK) complex. DDK plays essential roles in DNA replication initiation and check ...	This entry represents the BRCT domain found in Dbf4 protein. Dbf4 is a conserved eukaryotic protein that functions as the regulatory subunit of the Dbf4-dependent kinase (DDK) complex. DDK plays essential roles in DNA replication initiation and checkpoint activation. During the replication checkpoint, Saccharomyces cerevisiae Dbf4 is phosphorylated in a Rad53-dependent manner, and this, in turn, inhibits initiation of replication at late origins [1]. This entry represents the minimal region of Dbf4 required for the interaction with the checkpoint kinase Rad53 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	DBF4	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding DNA replication origin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding enzyme regulator activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding double-stranded DNA binding binding nucleic acid binding DNA replication origin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity	cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition response to stimulus signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication mitotic G2/M transition checkpoint regulation of mitotic cell cycle cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition response to stimulus signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication mitotic G2/M transition checkpoint regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle DNA replication checkpoint signaling regulation of cell cycle cell cycle process cell cycle G2/M phase transition regulation of biological process mitotic DNA replication checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process biological regulation DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition cellular process negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process sexual reproduction reproductive process meiotic cell cycle nuclear DNA replication cell cycle DNA replication meiotic cell cycle process premeiotic DNA replication cell division chromosome segregation negative regulation of exit from mitosis exit from mitosis cellular component organization cellular component organization or biogenesis mitotic nuclear division organelle fission nuclear division organelle organization regulation of exit from mitosis mitotic DNA replication regulation of DNA-templated DNA replication initiation positive regulation of mitotic cell cycle DNA replication positive regulation of DNA replication regulation of mitotic DNA replication initiation regulation of primary metabolic process positive regulation of metabolic process nuclear cell cycle DNA replication initiation positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of nuclear cell cycle DNA replication positive regulation of DNA metabolic process positive regulation of DNA-templated DNA replication regulation of metabolic process positive regulation of DNA-templated DNA replication initiation regulation of DNA replication regulation of DNA metabolic process cell cycle DNA replication initiation positive regulation of biological process mitotic DNA replication initiation positive regulation of nuclear cell cycle DNA replication positive regulation of cell cycle process positive regulation of mitotic cell cycle positive regulation of DNA replication initiation positive regulation of cellular process regulation of mitotic cell cycle DNA replication regulation of macromolecule metabolic process positive regulation of cell cycle regulation of DNA-templated DNA replication positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process positive regulation of protein modification process phosphate-containing compound metabolic process protein metabolic process positive regulation of protein phosphorylation protein modification process protein phosphorylation phosphorylation regulation of protein metabolic process macromolecule modification regulation of phosphorylation positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization regulation of reproductive process regulation of meiosis I meiosis I meiotic nuclear division positive regulation of reproductive process regulation of meiotic cell cycle positive regulation of nuclear division positive regulation of meiotic cell cycle regulation of organelle organization regulation of meiotic nuclear division meiosis I cell cycle process positive regulation of meiosis I regulation of nuclear division positive regulation of meiotic nuclear division DNA damage checkpoint signaling cellular response to stress response to stress mitotic DNA damage checkpoint signaling mitotic intra-S DNA damage checkpoint signaling DNA damage response signal transduction in response to DNA damage	intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton chromosome, centromeric region chromosome chromosomal region cytoplasm intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton chromosome, centromeric region chromosome chromosomal region cytoplasm chromatin membrane-bounded organelle protein-containing complex catalytic complex Dbf4-dependent protein kinase complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex protein kinase complex transferase complex, transferring phosphorus-containing groups serine/threonine protein kinase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR013939	Regulatory subunit Dfp1/Him1, central region	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR051590	DNA Replication Regulatory Kinase Subunit	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR006572	Zinc finger, DBF-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR038545	DBF-type zinc finger superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR036420	BRCT domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR055116	DBF4, BRCT domain	Domain

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.