Annotations: 5KBX

Co-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer signaling protein Ypd1 and the receiver domain of its downstream response regulator Ssk1

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)
A	d5kbxa_	All alpha proteins	Four-helical up-and-down bundle	Histidine-containing phosphotransfer domain, HPT domain	Phosphorelay protein-like	Phosphorelay protein ypd1	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d5kbxb_	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Histidine-containing phosphotransfer domain, HPT domain	8036546	3001634	SCOP2B (2022-06-29)
B	SCOP2 Family	CheY-related	8074354	4003632	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	CheY-like	8074355	3001156	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)
A	Acetyltransf_1	e5kbxA1	A: beta barrels	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Acetyltransf_1	ECOD (v294.2)
B	Acetyltransf_1	e5kbxB1	A: beta barrels	X: Beta domain of coronavirus spike glycoprotein	H: HAMP domain	T: Polymerase basic protein 2 cap-binding domain	F: Acetyltransf_1	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.160	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	HPT domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01627	Hpt domain (Hpt)	Hpt domain	The histidine-containing phosphotransfer (HPt) domain is a novel protein module with an active histidine residue that mediates phosphotransfer reactions in the two-component signaling systems. A multistep phosphorelay involving the HPt domain has bee ...	The histidine-containing phosphotransfer (HPt) domain is a novel protein module with an active histidine residue that mediates phosphotransfer reactions in the two-component signaling systems. A multistep phosphorelay involving the HPt domain has been suggested for these signaling pathways. The crystal structure of the HPt domain of the anaerobic sensor kinase ArcB has been determined [1]. The domain consists of six alpha helices containing a four-helix bundle-folding. The pattern of sequence similarity of the HPt domains of ArcB and components in other signaling systems can be interpreted in light of the three-dimensional structure and supports the conclusion that the HPt domains have a common structural motif both in prokaryotes and eukaryotes. In S. cerevisiae ypd1p this domain has been shown to contain a binding surface for Ssk1p (response regulator receiver domain containing protein Pfam:PF00072) [2].	Domain
B	PF00072	Response regulator receiver domain (Response_reg)	Response regulator receiver domain	This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Phosphorelay intermediate protein YPD1	transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein histidine kinase binding protein binding binding kinase binding enzyme binding protein kinase binding molecular transducer activity catalytic activity, acting on a protein kinase activity histidine phosphotransfer kinase activity protein kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein histidine kinase binding protein binding binding kinase binding enzyme binding protein kinase binding molecular transducer activity catalytic activity, acting on a protein kinase activity histidine phosphotransfer kinase activity protein kinase activity phosphotransferase activity, alcohol group as acceptor	cellular response to stimulus regulation of cellular process osmosensory signaling via phosphorelay pathway response to stimulus signaling cellular response to chemical stress intracellular signal transduction cellular response to environmental stimulus cell communication osmosensory signaling pathway cellular response to stress response to stress signal transduction response to osmotic stress cellular response to stimulus regulation of cellular process osmosensory signaling via phosphorelay pathway response to stimulus signaling cellular response to chemical stress intracellular signal transduction cellular response to environmental stimulus cell communication osmosensory signaling pathway cellular response to stress response to stress signal transduction response to osmotic stress regulation of biological process phosphorelay signal transduction system biological regulation cellular response to osmotic stress cellular response to chemical stimulus response to chemical cellular process response to abiotic stimulus cellular response to abiotic stimulus	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
B	Osmolarity two-component system protein SSK1	enzyme regulator 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 protein binding binding kinase binding mitogen-activated protein kinase kinase kinase binding enzyme binding protein kinase binding enzyme regulator 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 protein binding binding kinase binding mitogen-activated protein kinase kinase kinase binding enzyme binding protein kinase binding molecular transducer activity phosphorelay response regulator activity	cellular response to stimulus response to stimulus response to pH cellular response to pH response to abiotic stimulus cellular process cellular response to acidic pH response to acidic pH cellular response to abiotic stimulus cellular response to environmental stimulus regulation of cellular process osmosensory signaling via phosphorelay pathway signaling cellular response to chemical stress cellular response to stimulus response to stimulus response to pH cellular response to pH response to abiotic stimulus cellular process cellular response to acidic pH response to acidic pH cellular response to abiotic stimulus cellular response to environmental stimulus regulation of cellular process osmosensory signaling via phosphorelay pathway signaling cellular response to chemical stress intracellular signal transduction cell communication osmosensory signaling pathway cellular response to stress response to stress signal transduction response to osmotic stress regulation of biological process phosphorelay signal transduction system biological regulation cellular response to osmotic stress cellular response to chemical stimulus response to chemical regulation of signaling regulation of signal transduction regulation of MAPK cascade p38MAPK cascade regulation of intracellular signal transduction regulation of response to stimulus regulation of p38MAPK cascade intracellular signaling cassette MAPK cascade regulation of cell communication hyperosmotic response cellular hyperosmotic response regulation of cytoskeleton organization regulation of cellular component organization regulation of actin filament-based process actin cytoskeleton organization regulation of organelle organization cellular component organization organelle organization regulation of actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR045871	Histidine-containing phosphotransfer protein 1-5/Phosphorelay intermediate protein YPD1	Family
A	IPR036641	HPT domain superfamily	Homologous Superfamily
A	IPR008207	Signal transduction histidine kinase, phosphotransfer (Hpt) domain	Domain
B	IPR011006	CheY-like superfamily	Homologous Superfamily
B	IPR001789	Signal transduction response regulator, receiver 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.