4NKB | pdb_00004nkb

Crystal Structure of the cryptic polo box (CPB)of ZYG-1

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)
A		e4nkbA1	A: Ribosomal protein L41-A	X: Ribosomal protein L41-A	H: Ribosomal protein L41-A	T: Polo_box_2	F:	ECOD (20:10:01)
A		e4nkbA2	A: beta-Grasp	X: Uncharacterized protein TGAM_1934	H: Uncharacterized protein TGAM_1934	T:	F:	ECOD (20:10:01)
B		e4nkbB1	A: beta-Grasp	X: Uncharacterized protein TGAM_1934	H: Uncharacterized protein TGAM_1934	T:	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1120.120	Alpha Beta	2-Layer Sandwich	Arylsulfatase, C-terminal domain		CATH (4.3.0)
A	3.30.1120.130	Alpha Beta	2-Layer Sandwich	Arylsulfatase, C-terminal domain		CATH (4.3.0)
B	3.30.1120.120	Alpha Beta	2-Layer Sandwich	Arylsulfatase, C-terminal domain		CATH (4.3.0)
B	3.30.1120.130	Alpha Beta	2-Layer Sandwich	Arylsulfatase, C-terminal domain		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF18531	Polo box domain (Polo_box_2)	Polo box domain	In metazoans, Plk4 kinases control daughter centriole assembly. Plk4 homologs have an N-terminal kinase domain, a C-terminal polo box, and a central domain termed the 'cryptic polo box' (CPB) that has been shown to dimerize, to be sufficient for cent ...	In metazoans, Plk4 kinases control daughter centriole assembly. Plk4 homologs have an N-terminal kinase domain, a C-terminal polo box, and a central domain termed the 'cryptic polo box' (CPB) that has been shown to dimerize, to be sufficient for centriole localization and to be required for Plk4 to promote centriole assembly. Probable serine/threonine-protein kinase zyg-1 (EC:2.7.11.1) (ZYG-1) is a Plk4 homlog found in C. elegans. Crystal structure for the CPB of C. elegans ZYG-1, reveals that it forms a Z-shaped dimer containing an intermolecular beta-sheet with an extended basic surface patch. Electrostatic interactions between the basic patch on the ZYG-1 CPB dimer and the SPD-2 acidic region dock ZYG-1 onto centrioles to promote new centriole assembly. ZYG-1 CPB contains two tandem polo boxes (PB1 and PB2), each containing a six-stranded beta-sheet with an alpha-helix packed against one side [1].	Domain
A, B	PF18544	Polo box domain (Polo_box_3)	Polo box domain	In metazoans, Plk4 kinases control daughter centriole assembly. Plk4 homologs have an N-terminal kinase domain, a C-terminal polo box, and a central domain termed the 'cryptic polo box' (CPB) that has been shown to dimerize, to be sufficient for cent ...	In metazoans, Plk4 kinases control daughter centriole assembly. Plk4 homologs have an N-terminal kinase domain, a C-terminal polo box, and a central domain termed the 'cryptic polo box' (CPB) that has been shown to dimerize, to be sufficient for centriole localization and to be required for Plk4 to promote centriole assembly. Probable serine/threonine-protein kinase zyg-1 (EC:2.7.11.1) (ZYG-1) is a Plk4 homlog found in C. elegans. Crystal structure for the CPB of C. elegans ZYG-1, reveals that it forms a Z-shaped dimer containing an intermolecular beta-sheet with an extended basic surface patch. Electrostatic interactions between the basic patch on the ZYG-1 CPB dimer and the SPD-2 acidic region dock ZYG-1 onto centrioles to promote new centriole assembly. ZYG-1 CPB contains two tandem polo boxes (PB1 and PB2), each containing a six-stranded beta-sheet with an alpha-helix packed against one side [1]. This entry represents PB2.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Probable serine/threonine-protein kinase zyg-1	protein serine/threonine kinase activity eukaryotic translation initiation factor 2alpha kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine kinase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding protein serine/threonine kinase activity eukaryotic translation initiation factor 2alpha kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein serine kinase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding identical protein binding protein binding	cellular process cell cycle mitotic cell cycle regulation of cellular process regulation of cellular component organization positive regulation of centrosome duplication microtubule cytoskeleton organization positive regulation of biological process cellular component organization centrosome duplication centrosome cycle positive regulation of cell cycle process cellular component organization or biogenesis regulation of cell cycle cellular process cell cycle mitotic cell cycle regulation of cellular process regulation of cellular component organization positive regulation of centrosome duplication microtubule cytoskeleton organization positive regulation of biological process cellular component organization centrosome duplication centrosome cycle positive regulation of cell cycle process cellular component organization or biogenesis regulation of cell cycle positive regulation of cellular process cell cycle process regulation of biological process microtubule organizing center organization regulation of centrosome cycle regulation of cell cycle process biological regulation regulation of microtubule-based process positive regulation of cell cycle organelle organization regulation of centrosome duplication microtubule-based process cytoskeleton organization cell division positive regulation of organelle organization regulation of cytoskeleton organization positive regulation of cellular component organization positive regulation of spindle assembly membraneless organelle assembly cellular component biogenesis cellular component assembly chromosome segregation spindle organization organelle assembly positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of spindle organization regulation of cellular component biogenesis spindle assembly regulation of organelle organization regulation of spindle assembly regulation of organelle assembly regulation of microtubule cytoskeleton organization positive regulation of organelle assembly response to stimulus negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation response to stress negative regulation of cellular process translational initiation protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of translational initiation in response to stress regulation of biosynthetic process regulation of translational initiation regulation of protein metabolic process negative regulation of metabolic process negative regulation of translational initiation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process developmental process multicellular organismal process regulation of mitotic cell cycle, embryonic embryo development mitotic cell cycle, embryonic regulation of mitotic cell cycle multicellular organism development anatomical structure development centriole assembly centriole replication detection of external stimulus detection of stimulus detection of temperature stimulus response to external stimulus response to abiotic stimulus response to temperature stimulus detection of abiotic stimulus positive regulation of mitotic cell cycle, embryonic positive regulation of mitotic cell cycle protein localization to microtubule cytoskeleton regulation of localization regulation of protein localization regulation of protein localization to centrosome protein localization to microtubule organizing center localization macromolecule localization protein localization to cytoskeleton protein localization to organelle intracellular protein localization protein localization to centrosome cellular response to stimulus response to nutrient levels cellular response to amino acid starvation cellular response to starvation cellular response to nutrient levels cellular response to stress response to amino acid starvation response to starvation embryo development ending in birth or egg hatching regulation of cytokinesis cytoskeleton-dependent cytokinesis regulation of mitotic cytokinetic process mitotic cytokinetic process mitotic cytokinesis cytokinesis regulation of cytokinetic process regulation of cell division mitotic cell cycle process regulation of mitotic cytokinesis cytokinetic process protein localization to chromosome, centromeric region positive regulation of protein localization to kinetochore protein localization to kinetochore regulation of protein localization to kinetochore protein localization to chromosome protein localization to condensed chromosome positive regulation of protein localization positive regulation of signal transduction positive regulation of cell cycle checkpoint spindle checkpoint signaling regulation of signal transduction regulation of mitotic nuclear division intracellular signal transduction negative regulation of mitotic cell cycle regulation of cell cycle checkpoint negative regulation of mitotic sister chromatid segregation negative regulation of chromosome organization negative regulation of cell cycle phase transition mitotic spindle checkpoint signaling mitotic sister chromatid separation negative regulation of sister chromatid segregation mitotic spindle assembly checkpoint signaling sister chromatid segregation positive regulation of intracellular signal transduction regulation of mitotic sister chromatid segregation regulation of response to stimulus activation of mitotic cell cycle spindle assembly checkpoint negative regulation of mitotic nuclear division regulation of chromosome segregation regulation of mitotic sister chromatid separation spindle assembly checkpoint signaling regulation of mitotic metaphase/anaphase transition mitotic sister chromatid segregation negative regulation of mitotic metaphase/anaphase transition negative regulation of chromosome separation positive regulation of spindle checkpoint mitotic nuclear division regulation of signaling chromosome organization cell cycle checkpoint signaling negative regulation of chromosome segregation negative regulation of nuclear division chromosome separation negative regulation of metaphase/anaphase transition of cell cycle nuclear chromosome segregation regulation of cell communication positive regulation of cell communication regulation of cell cycle phase transition negative regulation of cell cycle cell communication signal transduction negative regulation of cellular component organization regulation of spindle checkpoint regulation of chromosome organization regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle spindle assembly checkpoint regulation of chromosome separation regulation of metaphase/anaphase transition of cell cycle regulation of mitotic spindle checkpoint signaling regulation of mitotic cell cycle spindle assembly checkpoint cell cycle phase transition positive regulation of response to stimulus regulation of intracellular signal transduction negative regulation of mitotic cell cycle phase transition organelle fission negative regulation of cell cycle process mitotic cell cycle checkpoint signaling nuclear division negative regulation of organelle organization regulation of sister chromatid segregation negative regulation of mitotic sister chromatid separation regulation of nuclear division metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition positive regulation of signaling	intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton centriole cytoplasm cytosol membrane-bounded organelle intracellular organelle centrosome microtubule organizing center cellular anatomical structure intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton centriole cytoplasm cytosol membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR040733	Zyg-1, polo box domain 1	Domain
A, B	IPR017441	Protein kinase, ATP binding site	Binding Site
A, B	IPR040734	Zyg-1, polo box domain 2	Domain
A, B	IPR008266	Tyrosine-protein kinase, active site	Active Site
A, B	IPR000719	Protein kinase domain	Domain
A, B	IPR046437	Serine/threonine-protein kinase, first cryptic polo-box domain superfamily	Homologous Superfamily
A, B	IPR047108	Plk4-like, second cryptic polo-box domain superfamily	Homologous Superfamily
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily

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.