1HD8 | pdb_00001hd8

Crystal structure of a deacylation-defective mutant of penicillin-binding protein 5 at 2.3 A resolution

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	d1hd8a1	All beta proteins	Penicillin-binding protein associated domain	Penicillin-binding protein associated domain	PBP5 C-terminal domain-like	Penicillin-binding protein 5, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1hd8a2	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	Penicillin-binding protein 5, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Penicillin-binding protein associated domain	8039109	3002006	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8039113	3001604	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)
A	Ricin_B_lectin, RicinB_lectin_2	e1hd8A1	A: alpha bundles	X: Cloacin translocation domain	H: beta-Prism I	T: beta-Prism I	F: Ricin_B_lectin, RicinB_lectin_2	ECOD (develop294)
A	Ion_trans_2	e1hd8A2	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Ion_trans_2	ECOD (develop294)
A	Transpeptidase	e1hd8A3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Transpeptidase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
A	2.60.410.10	Mainly Beta	Sandwich	Peptidoglycan synthesis regulatory factor (PBP3), Domain 2	D-Ala-D-Ala carboxypeptidase, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00768	D-alanyl-D-alanine carboxypeptidase (Peptidase_S11)	D-alanyl-D-alanine carboxypeptidase		Domain
A	PF07943	Penicillin-binding protein 5, C-terminal domain (PBP5_C)	Penicillin-binding protein 5, C-terminal domain	Penicillin-binding protein 5 expressed by E. coli (Swiss:P04287) functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain (Pfam:PF00768) is ...	Penicillin-binding protein 5 expressed by E. coli (Swiss:P04287) functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain (Pfam:PF00768) is the catalytic domain. The C-terminal domain featured in this family is organised into a sandwich of two anti-parallel beta-sheets, and has a relatively hydrophobic surface as compared to the N-terminal domain. Its precise function is unknown; it may mediate interactions with other cell wall-synthesising enzymes, thus allowing the protein to be recruited to areas of active cell wall synthesis. It may also function as a linker domain that positions the active site in the catalytic domain closer to the peptidoglycan layer, to allow it to interact with cell wall peptides [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PENICILLIN-BINDING PROTEIN 5	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 identical protein binding protein binding protein homodimerization activity protein dimerization activity 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 identical protein binding protein binding protein homodimerization activity protein dimerization activity beta-lactamase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds peptidase activity catalytic activity, acting on a protein exopeptidase activity carboxypeptidase activity serine-type exopeptidase activity serine hydrolase activity serine-type D-Ala-D-Ala carboxypeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity	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 glycosaminoglycan metabolic process aminoglycan metabolic process peptidoglycan metabolic process 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 glycosaminoglycan metabolic process aminoglycan metabolic process peptidoglycan metabolic process carbohydrate derivative metabolic process metabolic process cellular process macromolecule metabolic process cell division cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis macromolecule biosynthetic process cellular component biogenesis peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan biosynthetic process glycosaminoglycan biosynthetic process cell wall macromolecule metabolic process proteolysis primary metabolic process protein metabolic process	cell periphery cellular anatomical structure plasma membrane membrane outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR012907	Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal	Domain
A	IPR018044	Peptidase S11, D-alanyl-D-alanine carboxypeptidase A	Family
A	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A	IPR015956	Penicillin-binding protein, C-terminal domain superfamily	Homologous Superfamily
A	IPR037167	D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily	Homologous Superfamily
A	IPR001967	Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.