3N25

The structure of muscle pyruvate kinase in complex with proline, pyruvate, and Mn2+

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	PK beta-barrel domain-like	8042524	3001296	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PK C-terminal domain-like	8044402	3000442	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PK beta-barrel domain-like	8042524	3001296	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PK C-terminal domain-like	8044402	3000442	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PK C-terminal domain-like	8044402	3000442	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PK beta-barrel domain-like	8042524	3001296	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PK C-terminal domain-like	8044402	3000442	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PK beta-barrel domain-like	8042524	3001296	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PK beta-barrel domain-like	8042524	3001296	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PK C-terminal domain-like	8044402	3000442	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PK beta-barrel domain-like	8042524	3001296	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PK C-terminal domain-like	8044402	3000442	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	PK C-terminal domain-like	8044402	3000442	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	PK beta-barrel domain-like	8042524	3001296	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	PK beta-barrel domain-like	8042524	3001296	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	PK C-terminal domain-like	8044402	3000442	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Phosphoenolpyruvate/pyruvate domain	8043639	3000510	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	PK_2nd	e3n25D4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PK beta-barrel domain-like	F: PK_2nd	ECOD (1.6)
D	PK_1st	e3n25D3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PK_1st	ECOD (1.6)
D	PK_C	e3n25D1	A: a/b three-layered sandwiches	X: PK C-terminal domain-like (From Topology)	H: PK C-terminal domain-like (From Topology)	T: PK C-terminal domain-like	F: PK_C	ECOD (1.6)
A	PK_2nd	e3n25A4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PK beta-barrel domain-like	F: PK_2nd	ECOD (1.6)
A	PK_1st	e3n25A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PK_1st	ECOD (1.6)
A	PK_C	e3n25A3	A: a/b three-layered sandwiches	X: PK C-terminal domain-like (From Topology)	H: PK C-terminal domain-like (From Topology)	T: PK C-terminal domain-like	F: PK_C	ECOD (1.6)
B	PK_2nd	e3n25B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PK beta-barrel domain-like	F: PK_2nd	ECOD (1.6)
B	PK_1st	e3n25B3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PK_1st	ECOD (1.6)
B	PK_C	e3n25B2	A: a/b three-layered sandwiches	X: PK C-terminal domain-like (From Topology)	H: PK C-terminal domain-like (From Topology)	T: PK C-terminal domain-like	F: PK_C	ECOD (1.6)
C	PK_2nd	e3n25C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PK beta-barrel domain-like	F: PK_2nd	ECOD (1.6)
C	PK_1st	e3n25C2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PK_1st	ECOD (1.6)
C	PK_C	e3n25C3	A: a/b three-layered sandwiches	X: PK C-terminal domain-like (From Topology)	H: PK C-terminal domain-like (From Topology)	T: PK C-terminal domain-like	F: PK_C	ECOD (1.6)
E	PK_2nd	e3n25E1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PK beta-barrel domain-like	F: PK_2nd	ECOD (1.6)
E	PK_1st	e3n25E3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PK_1st	ECOD (1.6)
E	PK_C	e3n25E2	A: a/b three-layered sandwiches	X: PK C-terminal domain-like (From Topology)	H: PK C-terminal domain-like (From Topology)	T: PK C-terminal domain-like	F: PK_C	ECOD (1.6)
F	PK_2nd	e3n25F1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PK beta-barrel domain-like	F: PK_2nd	ECOD (1.6)
F	PK_1st	e3n25F3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PK_1st	ECOD (1.6)
F	PK_C	e3n25F2	A: a/b three-layered sandwiches	X: PK C-terminal domain-like (From Topology)	H: PK C-terminal domain-like (From Topology)	T: PK C-terminal domain-like	F: PK_C	ECOD (1.6)
G	PK_2nd	e3n25G1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PK beta-barrel domain-like	F: PK_2nd	ECOD (1.6)
G	PK_1st	e3n25G2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PK_1st	ECOD (1.6)
G	PK_C	e3n25G3	A: a/b three-layered sandwiches	X: PK C-terminal domain-like (From Topology)	H: PK C-terminal domain-like (From Topology)	T: PK C-terminal domain-like	F: PK_C	ECOD (1.6)
H	PK_2nd	e3n25H4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PK beta-barrel domain-like	F: PK_2nd	ECOD (1.6)
H	PK_1st	e3n25H3	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PK_1st	ECOD (1.6)
H	PK_C	e3n25H1	A: a/b three-layered sandwiches	X: PK C-terminal domain-like (From Topology)	H: PK C-terminal domain-like (From Topology)	T: PK C-terminal domain-like	F: PK_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.1380.20	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate Kinase	Chain: A, domain 1	CATH (4.3.0)
D	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
D	2.40.33.10	Mainly Beta	Beta Barrel	M1 Pyruvate Kinase	Domain 3	CATH (4.3.0)
A	3.40.1380.20	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate Kinase	Chain: A, domain 1	CATH (4.3.0)
A	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
A	2.40.33.10	Mainly Beta	Beta Barrel	M1 Pyruvate Kinase	Domain 3	CATH (4.3.0)
B	3.40.1380.20	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate Kinase	Chain: A, domain 1	CATH (4.3.0)
B	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
B	2.40.33.10	Mainly Beta	Beta Barrel	M1 Pyruvate Kinase	Domain 3	CATH (4.3.0)
C	3.40.1380.20	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate Kinase	Chain: A, domain 1	CATH (4.3.0)
C	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
C	2.40.33.10	Mainly Beta	Beta Barrel	M1 Pyruvate Kinase	Domain 3	CATH (4.3.0)
E	3.40.1380.20	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate Kinase	Chain: A, domain 1	CATH (4.3.0)
E	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
E	2.40.33.10	Mainly Beta	Beta Barrel	M1 Pyruvate Kinase	Domain 3	CATH (4.3.0)
F	3.40.1380.20	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate Kinase	Chain: A, domain 1	CATH (4.3.0)
F	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
F	2.40.33.10	Mainly Beta	Beta Barrel	M1 Pyruvate Kinase	Domain 3	CATH (4.3.0)
G	3.40.1380.20	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate Kinase	Chain: A, domain 1	CATH (4.3.0)
G	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
G	2.40.33.10	Mainly Beta	Beta Barrel	M1 Pyruvate Kinase	Domain 3	CATH (4.3.0)
H	3.40.1380.20	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate Kinase	Chain: A, domain 1	CATH (4.3.0)
H	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
H	2.40.33.10	Mainly Beta	Beta Barrel	M1 Pyruvate Kinase	Domain 3	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	PF02887	Pyruvate kinase, alpha/beta domain (PK_C)	Pyruvate kinase, alpha/beta domain	Pyruvate kinase catalyses the final step in glycolysis, the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP [1,2]. The structure of several pyruvate kinases from various organisms have been determined [2, ...	Pyruvate kinase catalyses the final step in glycolysis, the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP [1,2]. The structure of several pyruvate kinases from various organisms have been determined [2, 3,4]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain (represented in this entry). This domain is at the C-terminal of pyruvate kinases and contains the FBP (fructose 1,6-bisphosphate) binding site [2,4,5].	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF00224	Pyruvate kinase, barrel domain (PK)	Pyruvate kinase, barrel domain	This is the barrel domain of pyruvate kinases. This domain represents the beta/alpha barrel and the small beta-barrel domain inserted within it. The active site is found in a cleft between the two domains [1,2,3,4].	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	Pyruvate kinase isozymes M1/M2	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding potassium ion binding alkali metal ion binding RNA binding nucleic acid binding mRNA binding pyruvate kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity	regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of cytoplasmic translation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of cytoplasmic translation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of translation cytoplasmic translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of cytoplasmic translation regulation of metabolic process multicellular organismal process regulation of sprouting angiogenesis regulation of developmental process angiogenesis regulation of vasculature development positive regulation of developmental process multicellular organism development tube morphogenesis anatomical structure development positive regulation of sprouting angiogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development developmental process regulation of multicellular organismal development blood vessel morphogenesis tube development positive regulation of angiogenesis sprouting angiogenesis vasculature development circulatory system development anatomical structure morphogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis positive regulation of multicellular organismal process phosphorylation phosphate-containing compound metabolic process phosphorus metabolic process cellular response to nitrogen compound cellular response to stimulus response to stimulus response to endogenous stimulus response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to insulin cellular response to insulin stimulus cellular response to hormone stimulus	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle rough endoplasmic reticulum endoplasmic reticulum cytoplasm endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015795	Pyruvate kinase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015813	Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011037	Pyruvate kinase-like, insert domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015806	Pyruvate kinase, insert domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036918	Pyruvate kinase, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001697	Pyruvate kinase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018209	Pyruvate kinase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR040442	Pyruvate kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015793	Pyruvate kinase, barrel	Domain

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3N25

The structure of muscle pyruvate kinase in complex with proline, pyruvate, and Mn2+

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage