1PYY | pdb_00001pyy

Double mutant PBP2x T338A/M339F from Streptococcus pneumoniae strain R6 at 2.4 A resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d1pyya1	Alpha and beta proteins (a+b)	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
A	d1pyya3	Alpha and beta proteins (a+b)	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	Penicillin-binding protein 2x (pbp-2x), N-terminal domain	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)
A	d1pyya4	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	Penicillin-binding protein 2x (pbp-2x), transpeptidase domain	(Streptococcus pneumoniae R6 ) [TaxId: 171101 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PBP_dimer	e1pyyA1	A: beta complex topology	X: Penicillin binding protein dimerisation domain (From Topology)	H: Penicillin binding protein dimerisation domain (From Topology)	T: Penicillin binding protein dimerisation domain	F: PBP_dimer	ECOD (1.6)
A	Transpeptidase_1st_1	e1pyyA2	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_1st_1	ECOD (1.6)
A	PASTA_2	e1pyyA3	A: a+b two layers	X: CI-2 family of serine protease inhibitors-like	H: Penicillin-binding protein 2x (pbp-2x)-C (From Topology)	T: Penicillin-binding protein 2x (pbp-2x)-C	F: PASTA_2	ECOD (1.6)
A	PASTA_1	e1pyyA4	A: a+b two layers	X: CI-2 family of serine protease inhibitors-like	H: Penicillin-binding protein 2x (pbp-2x)-C (From Topology)	T: Penicillin-binding protein 2x (pbp-2x)-C	F: PASTA_1	ECOD (1.6)
A	PBP_2x_ClpS	e1pyyA5	A: a+b two layers	X: ClpS-like	H: Penicillin binding protein ClpS-like domain (From Topology)	T: Penicillin binding protein ClpS-like domain	F: PBP_2x_ClpS	ECOD (1.6)
A	Transpeptidase_2nd	e1pyyA6	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.1310.10	Alpha Beta	Alpha-Beta Complex	Penicillin-binding protein 2a (Domain 2)	Penicillin-binding protein 2a (Domain 2)	CATH (4.3.0)
A	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00905	Penicillin binding protein transpeptidase domain (Transpeptidase)	Penicillin binding protein transpeptidase domain	The active site serine (residue 337 in Swiss:P14677) is conserved in all members of this family.	Domain
A	PF03793	PASTA domain (PASTA)	PASTA domain	This domain is found at the C termini of several Penicillin-binding proteins and bacterial serine/threonine kinases [1]. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. It is a smal ...	This domain is found at the C termini of several Penicillin-binding proteins and bacterial serine/threonine kinases [1]. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Penicillin-binding protein 2X	amide binding organic acid binding binding ion binding anion binding penicillin binding carboxylic acid binding heterocyclic compound binding monocarboxylic acid binding small molecule binding sulfur compound binding	developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis cellular process cell division cellular component organization developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis cellular process cell division cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization response to stimulus response to chemical response to antibiotic carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process cellular component biogenesis peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process metabolic process glycosaminoglycan biosynthetic process macromolecule metabolic process	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A	IPR050515	Bacterial Transpeptidases and Beta-Lactamases	Family
A	IPR036138	Penicillin-binding protein, dimerisation domain superfamily	Homologous Superfamily
A	IPR005543	PASTA domain	Domain
A	IPR053467	Bacterial Transpeptidase	Family
A	IPR005311	Penicillin-binding protein, dimerisation domain	Domain
A	IPR001460	Penicillin-binding protein, transpeptidase	Domain

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.