5LP5 | pdb_00005lp5

Complex between Penicillin-Binding Protein (PBP2) and MreC from Helicobacter pylori

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e5lp5B1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: Abhydrolase_3, BD-FAE	F:	ECOD (20:10:01)
A		e5lp5A1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: Abhydrolase_3, BD-FAE	F:	ECOD (20:10:01)
F		e5lp5F1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: FATC	F:	ECOD (20:10:01)
E		e5lp5E1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: FATC	F:	ECOD (20:10:01)
D		e5lp5D1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: FATC	F:	ECOD (20:10:01)
C		e5lp5C1	A: TIM beta/alpha-barrel	X: TIM barrels	H: TIM barrels	T: Abhydrolase_3, BD-FAE	F:	ECOD (20:10:01)

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
C, D, E, F	PF04085	Rod shape-determining protein MreC, barrel core (MreC)	Rod shape-determining protein MreC, barrel core	MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped [1]. This entry represents the periplasmic core of these proteins which is ...	MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped [1]. This entry represents the periplasmic core of these proteins which is composed of two six-stranded beta-barrels [1,2]. MreC self-associates into polar filaments [1]. The periplasmic part of MreC contains also a coiled-coil region which is involved in the formation of dimer essential for its function [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Penicillin-binding protein 2 (Pbp2)	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 organic acid binding binding ion 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 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 serine-type D-Ala-D-Ala carboxypeptidase 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 cellular component organization cell wall organization or biogenesis cell wall 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 component organization cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization 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 wall macromolecule metabolic process proteolysis primary metabolic process protein metabolic process	cell periphery cellular anatomical structure plasma membrane membrane
C, D, E, F	Rod shape-determining protein (MreC)	-	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B	IPR017790	Penicillin-binding protein 2	Family
A, B	IPR036138	Penicillin-binding protein, dimerisation domain superfamily	Homologous Superfamily
A, B	IPR005311	Penicillin-binding protein, dimerisation domain	Domain
A, B	IPR001460	Penicillin-binding protein, transpeptidase	Domain
A, B	IPR050515	Class D beta-lactamase/transpeptidase	Family
C, D, E, F	IPR055342	Rod shape-determining protein MreC, beta-barrel core	Domain
C, D, E, F	IPR007221	Rod shape-determining protein MreC	Family
C, D, E, F	IPR042175	Cell/Rod shape-determining protein MreC, domain 2	Homologous Superfamily

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.