5UWV

Crystal structure of Mycobacterium abscessus L,D-transpeptidase 2

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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 [auth A]	LDT_IgD_like_2	e5uwvA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: LDT_IgD_like_2	ECOD (1.6)
B [auth A]	YkuD	e5uwvA2	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 [auth D]	LDT_IgD_like_2	e5uwvD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: LDT_IgD_like_2	ECOD (1.6)
C [auth D]	YkuD	e5uwvD2	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)
D [auth E]	LDT_IgD_like_2	e5uwvE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: LDT_IgD_like_2	ECOD (1.6)
D [auth E]	YkuD	e5uwvE1	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)
E [auth C]	LDT_IgD_like_2	e5uwvC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: LDT_IgD_like_2	ECOD (1.6)
E [auth C]	YkuD	e5uwvC2	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)
F	LDT_IgD_like_2	e5uwvF2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: LDT_IgD_like_2	ECOD (1.6)
F	YkuD	e5uwvF1	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 [auth B]	LDT_IgD_like_2	e5uwvB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: LDT_IgD_like_2	ECOD (1.6)
A [auth B]	YkuD	e5uwvB2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	2.60.40.3710	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
B [auth A]	2.40.440.10	Mainly Beta	Beta Barrel	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	CATH (4.3.0)
C [auth D]	2.60.40.3710	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
C [auth D]	2.40.440.10	Mainly Beta	Beta Barrel	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	CATH (4.3.0)
D [auth E]	2.60.40.3710	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
D [auth E]	2.40.440.10	Mainly Beta	Beta Barrel	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	CATH (4.3.0)
E [auth C]	2.60.40.3710	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
E [auth C]	2.40.440.10	Mainly Beta	Beta Barrel	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	CATH (4.3.0)
F	2.60.40.3710	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
F	2.40.440.10	Mainly Beta	Beta Barrel	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	CATH (4.3.0)
A [auth B]	2.60.40.3710	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A [auth B]	2.40.440.10	Mainly Beta	Beta Barrel	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A], C [auth D], D [auth E], E [auth C], A [auth B], B [auth A], C [auth D], D [auth E], E [auth C], F	PF17964	Bacterial Ig domain (Big_10)	Bacterial Ig domain	This entry represents a bacterial Ig-like domain found associated with transpeptidase domains [1].	Domain
A [auth B], B [auth A], C [auth D], D [auth E], E [auth C], A [auth B], B [auth A], C [auth D], D [auth E], E [auth C], F	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 [auth B], B [auth A], C [auth D], D [auth E], E [auth C], A [auth B], B [auth A], C [auth D], D [auth E], E [auth C], F	L,D-TRANSPEPTIDASE 2	acyltransferase activity transferase activity catalytic 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 cellular biosynthetic 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 carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cellular biosynthetic process cell wall organization or biogenesis glycosaminoglycan metabolic process cellular 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 cellular process metabolic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis macromolecule metabolic process cellular component organization cell wall organization external encapsulating structure organization	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A], C [auth D], D [auth E], E [auth C], A [auth B], B [auth A], C [auth D], D [auth E], E [auth C], F	IPR050979	Bacterial L,D-transpeptidase	Family
A [auth B], B [auth A], C [auth D], D [auth E], E [auth C], A [auth B], B [auth A], C [auth D], D [auth E], E [auth C], F	IPR041280	Bacterial Ig domain, transpeptidase-associated	Domain
A [auth B], B [auth A], C [auth D], D [auth E], E [auth C], A [auth B], B [auth A], C [auth D], D [auth E], E [auth C], F	IPR005490	L,D-transpeptidase catalytic domain	Domain
A [auth B], B [auth A], C [auth D], D [auth E], E [auth C], A [auth B], B [auth A], C [auth D], D [auth E], E [auth C], F	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.