3ZG5

Crystal structure of PBP2a from MRSA in complex with peptidoglycan analogue at allosteric

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
AMR Gene: CARD Annotation
AMR Gene Family: CARD Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3zg5a1	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
A	d3zg5a2	Alpha and beta proteins (a+b)	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
A	d3zg5a3	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
B	d3zg5b1	Alpha and beta proteins (a+b)	Cystatin-like	NTF2-like	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
B	d3zg5b2	Alpha and beta proteins (a+b)	Penicillin binding protein dimerisation domain	Penicillin binding protein dimerisation domain	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
B	d3zg5b3	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	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	e3zg5A5	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	e3zg5A1	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	ECOD (1.6)
A	MecA_N	e3zg5A7	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: MecA_N	ECOD (1.6)
A	EUF08385	e3zg5A6	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: EUF08385	ECOD (1.6)
A	Transpeptidase_2nd	e3zg5A3	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)
B	PBP_dimer	e3zg5B5	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)
B	Transpeptidase_1st	e3zg5B1	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	ECOD (1.6)
B	MecA_N	e3zg5B7	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: MecA_N	ECOD (1.6)
B	EUF08385	e3zg5B6	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: EUF08385	ECOD (1.6)
B	Transpeptidase_2nd	e3zg5B3	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	3.10.450.100	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
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	3.30.1390.30	Alpha Beta	2-Layer Sandwich	Ribosomal Protein L30	Chain: A,	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)
B	3.10.450.100	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
B	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)
B	3.30.1390.30	Alpha Beta	2-Layer Sandwich	Ribosomal Protein L30	Chain: A,	CATH (4.3.0)
B	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A, B	ARO:3000617	mecA	A foreign PBP2a acquired by lateral gene transfer that is able to perform peptidoglycan synthesis in the presence of beta-lactams.	CARD (3.3.0)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A, B	ARO:3001208	methicillin resistant PBP2	penam	antibiotic target replacement	CARD (3.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03717	Penicillin-binding Protein dimerisation domain (PBP_dimer)	Penicillin-binding Protein dimerisation domain	This domain is found at the N terminus of Class B High Molecular Weight Penicillin-Binding Proteins. Its function has not been precisely defined, but is strongly implicated in PBP polymerisation. The domain forms a largely disordered 'sugar tongs' st ...	This domain is found at the N terminus of Class B High Molecular Weight Penicillin-Binding Proteins. Its function has not been precisely defined, but is strongly implicated in PBP polymerisation. The domain forms a largely disordered 'sugar tongs' structure.	Domain
A, B	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, B	PF05223	NTF2-like N-terminal transpeptidase domain (MecA_N)	NTF2-like N-terminal transpeptidase domain	The structure of this domain from MecA is known [1] Swiss:Q53707 and is found to be similar to that found in NTF2 Pfam:PF02136. This domain seems unlikely to have an enzymatic function, and its role remains unknown.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	PEPTIDOGLYCAN ANALOGUE	-	-	-
A, B	Penicillin binding protein 2 prime	serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity hydrolase activity peptidoglycan L,D-transpeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity exopeptidase activity catalytic activity carboxypeptidase activity amide binding organic acid binding binding serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity hydrolase activity peptidoglycan L,D-transpeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity exopeptidase activity catalytic activity carboxypeptidase activity amide binding organic acid binding binding ion binding organic cyclic compound binding anion binding penicillin binding carboxylic acid binding heterocyclic compound binding monocarboxylic acid binding small molecule binding sulfur compound binding	cellular component organization cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization response to stimulus response to chemical response to antibiotic	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR032710	NTF2-like domain superfamily	Homologous Superfamily
A, B	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B	IPR005311	Penicillin-binding protein, dimerisation domain	Domain
A, B	IPR001460	Penicillin-binding protein, transpeptidase	Domain
A, B	IPR050515	Bacterial Transpeptidases and Beta-Lactamases	Family
A, B	IPR007887	NTF2-like N-terminal transpeptidase	Domain
A, B	IPR036138	Penicillin-binding protein, dimerisation domain superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	DAL	RESID: AA0111 , AA0191 PSI-MOD : meso-lanthionine MOD:00120 , D-alanine (Ala) MOD:00198 , D-alanine (Ser) MOD:00858 , D-alanine MOD:00862
C, D	FGA	RESID: AA0111 , AA0191

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.