2HKL | pdb_00002hkl

Crystal structure of Enterococcus faecium L,D-transpeptidase C442S mutant

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)
C	d2hklc2	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase, C-terminal, catalytic domain	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)
C	d2hklc1	Alpha and beta proteins (a+b)	L,D-transpeptidase pre-catalytic domain-like	L,D-transpeptidase pre-catalytic domain-like	L,D-transpeptidase pre-catalytic domain-like	L,D-transpeptidase, pre-catalytic domain	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)
B	d2hklb2	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase, C-terminal, catalytic domain	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)
B	d2hklb1	Alpha and beta proteins (a+b)	L,D-transpeptidase pre-catalytic domain-like	L,D-transpeptidase pre-catalytic domain-like	L,D-transpeptidase pre-catalytic domain-like	L,D-transpeptidase, pre-catalytic domain	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)
A	d2hkla2	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase, C-terminal, catalytic domain	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)
A	d2hkla1	Alpha and beta proteins (a+b)	L,D-transpeptidase pre-catalytic domain-like	L,D-transpeptidase pre-catalytic domain-like	L,D-transpeptidase pre-catalytic domain-like	L,D-transpeptidase, pre-catalytic domain	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	L, D-transpeptidase catalytic domain-like	8035519	3000695	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	L, D-transpeptidase pre-catalytic domain-like	8035521	3000360	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	L, D-transpeptidase pre-catalytic domain-like	8035521	3000360	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	L, D-transpeptidase catalytic domain-like	8035519	3000695	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	L, D-transpeptidase pre-catalytic domain-like	8035521	3000360	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	L, D-transpeptidase catalytic domain-like	8035519	3000695	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)
C	YkuD	e2hklC1	A: beta complex topology	X: L,D-transpeptidase catalytic domain-like (From Topology)	H: L,D-transpeptidase catalytic domain-like (From Topology)	T: L,D-transpeptidase catalytic domain-like	F: YkuD	ECOD (1.6)
C	PG_binding_4	e2hklC2	A: a+b complex topology	X: L,D-transpeptidase pre-catalytic domain-like (From Topology)	H: L,D-transpeptidase pre-catalytic domain-like (From Topology)	T: L,D-transpeptidase pre-catalytic domain-like	F: PG_binding_4	ECOD (1.6)
B	YkuD	e2hklB1	A: beta complex topology	X: L,D-transpeptidase catalytic domain-like (From Topology)	H: L,D-transpeptidase catalytic domain-like (From Topology)	T: L,D-transpeptidase catalytic domain-like	F: YkuD	ECOD (1.6)
B	PG_binding_4	e2hklB2	A: a+b complex topology	X: L,D-transpeptidase pre-catalytic domain-like (From Topology)	H: L,D-transpeptidase pre-catalytic domain-like (From Topology)	T: L,D-transpeptidase pre-catalytic domain-like	F: PG_binding_4	ECOD (1.6)
A	YkuD	e2hklA1	A: beta complex topology	X: L,D-transpeptidase catalytic domain-like (From Topology)	H: L,D-transpeptidase catalytic domain-like (From Topology)	T: L,D-transpeptidase catalytic domain-like	F: YkuD	ECOD (1.6)
A	PG_binding_4	e2hklA2	A: a+b complex topology	X: L,D-transpeptidase pre-catalytic domain-like (From Topology)	H: L,D-transpeptidase pre-catalytic domain-like (From Topology)	T: L,D-transpeptidase pre-catalytic domain-like	F: PG_binding_4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.10.20.800	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.2.0)
C	2.40.440.10	Mainly Beta	Beta Barrel	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	CATH (4.2.0)
B	3.10.20.800	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.2.0)
B	2.40.440.10	Mainly Beta	Beta Barrel	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	CATH (4.2.0)
A	3.10.20.800	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.2.0)
A	2.40.440.10	Mainly Beta	Beta Barrel	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF12229	Putative peptidoglycan binding domain (PG_binding_4)	Putative peptidoglycan binding domain	This domain is found associated with the L,D-transpeptidase domain Pfam:PF03734. The structure of this domain has been solved and shows a mixed alpha-beta fold composed of nine beta strands and four alpha helices. This domain is usually found to be ...	This domain is found associated with the L,D-transpeptidase domain Pfam:PF03734. The structure of this domain has been solved and shows a mixed alpha-beta fold composed of nine beta strands and four alpha helices. This domain is usually found to be duplicated. Therefore, it seems likely that this domain acts to bind the two unlinked peptidoglycan chains and bring them into close association so they can be cross linked by the transpeptidase domain (Bateman A pers. observation).	Domain
A, B, C	PF03734	L,D-transpeptidase catalytic domain (YkuD)	L,D-transpeptidase catalytic domain	This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking [1]. This gives bacteria resistance to beta-lacta ...	This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking [1]. This gives bacteria resistance to beta-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. Several members of this family contain peptidoglycan binding domains. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	L,D-TRANSPEPTIDASE	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 transferase 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 carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis 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 carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process cellular component biogenesis peptidoglycan-protein cross-linking peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process cellular process metabolic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis macromolecule metabolic process cell wall macromolecule metabolic process cellular component organization cell wall organization external encapsulating structure organization	cellular anatomical structure membrane extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR038054	L,D-transpeptidase central domain-like superfamily	Homologous Superfamily
A, B, C	IPR022029	YoaR-like, putative peptidoglycan binding domain	Domain
A, B, C	IPR050979	Bacterial L,D-transpeptidase	Family
A, B, C	IPR005490	L,D-transpeptidase catalytic domain	Domain
A, B, C	IPR038063	L,D-transpeptidase catalytic domain-like	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.