3VYO

Crystal structure of Mycobacterium tuberculosis L,D-transpeptidase LdtMt2 N140 truncation mutant (resideus 140-408)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
B	d3vyob1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d3vyob2	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d3vyoa1	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	automated matches	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d3vyoa2	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	automated matches	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	LDT_IgD_like_2	e3vyoB1	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	YkuD	e3vyoB2	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	LDT_IgD_like_2	e3vyoA1	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	YkuD	e3vyoA2	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	2.60.40.3710	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
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)
A	2.60.40.3710	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	Probable conserved lipoprotein LPPS	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 acyltransferase activity transferase activity cation 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 acyltransferase activity transferase activity cation binding ion binding binding metal ion binding small molecule binding	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 cellular component organization cell wall organization external encapsulating structure organization	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR050979	Bacterial L,D-transpeptidase	Family
A, B	IPR041280	Bacterial Ig domain, transpeptidase-associated	Domain
A, B	IPR005490	L,D-transpeptidase catalytic domain	Domain
A, B	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.