4FXF | pdb_00004fxf

Structure of M2 pyruvate kinase in complex with phenylalanine

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth B]	PK	e4fxfB2	A: alpha bundles	X: Alpha-beta plaits	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: PK	ECOD (develop294)
C	PK	e4fxfC1	A: alpha bundles	X: Alpha-beta plaits	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: PK	ECOD (develop294)
B [auth D]	PK	e4fxfD1	A: alpha bundles	X: Alpha-beta plaits	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: PK	ECOD (develop294)
A	PK	e4fxfA1	A: alpha bundles	X: Alpha-beta plaits	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: PK	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	3.40.1380.20	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate Kinase	Chain: A, domain 1	CATH (4.3.0)
D [auth B]	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
D [auth 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)
B [auth D]	3.40.1380.20	Alpha Beta	3-Layer(aba) Sandwich	Pyruvate Kinase	Chain: A, domain 1	CATH (4.3.0)
B [auth D]	3.20.20.60	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Phosphoenolpyruvate-binding domains	CATH (4.3.0)
B [auth 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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth D], C, D [auth B]	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
A, B [auth D], C, D [auth B]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth D], C, D [auth B]	Pyruvate kinase isozymes M1/M2	cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity protein-containing complex binding MHC protein complex binding cation binding ion binding binding potassium ion binding alkali metal ion binding metal ion binding small molecule binding transcription coactivator activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity protein-containing complex binding MHC protein complex binding MHC class II protein complex binding RNA binding nucleic acid binding protein tyrosine 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 magnesium ion binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding mRNA binding non-membrane spanning protein tyrosine kinase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity cell adhesion molecule binding cadherin binding protein serine/threonine kinase activity histone H3 kinase activity histone modifying activity histone H3T11 kinase activity histone kinase activity pyruvate kinase activity	cellular process cell death programmed cell death ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process nucleobase-containing compound metabolic process glycolytic process cellular process cell death programmed cell death ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process nucleobase-containing compound metabolic process glycolytic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process purine nucleoside diphosphate metabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration catabolic process ATP metabolic process energy derivation by oxidation of organic compounds purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process generation of precursor metabolites and energy purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation protein biosynthetic process 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 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 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 cellular response to stimulus cellular response to nitrogen compound 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 glucose catabolic process to pyruvate hexose catabolic process hexose metabolic process glucose catabolic process monosaccharide catabolic process small molecule catabolic process monosaccharide metabolic process canonical glycolysis glycolytic process through glucose-6-phosphate glycolytic process through fructose-6-phosphate glucose metabolic process positive regulation of DNA-templated transcription RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol cell projection sperm principal piece cilium 9+2 motile cilium sperm flagellum motile cilium plasma membrane bounded cell projection membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule endomembrane system intracellular organelle lumen organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle nucleus nucleoplasm nuclear lumen rough endoplasmic reticulum endoplasmic reticulum vesicle lumen cytoplasmic vesicle lumen secretory granule lumen

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B [auth D], C, D [auth B]	Pharos: P14618	Neoplasm Invasiveness osteoporosis sarcomatoid carcinoma carcinoma malignant ependymoma mammary neoplasms, animal osteosarcoma adrenal cortex adenoma pancreatic intraductal papillary-mucinous carcinoma psoriasis breast carcinoma glioblastoma invasive ductal breast carcinoma lung adenocarcinoma malignant pancreatic neoplasm Neoplasm Invasiveness osteoporosis sarcomatoid carcinoma carcinoma malignant ependymoma mammary neoplasms, animal osteosarcoma adrenal cortex adenoma pancreatic intraductal papillary-mucinous carcinoma psoriasis breast carcinoma glioblastoma invasive ductal breast carcinoma lung adenocarcinoma malignant pancreatic neoplasm non-small cell lung carcinoma ovarian cancer adrenal cortex carcinoma pancreatic intraductal papillary-mucinous neoplasm astrocytic tumor cancer ulcerative colitis dermatomyositis hepatocellular carcinoma large cell medulloblastoma lung cancer medulloblastoma oligodendroglioma pancreatic ductal adenocarcinoma atypical teratoid rhabdoid tumor rheumatoid arthritis undifferentiated carcinoma ductal breast carcinoma in situ interstitial lung disease

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.