1Y7M | pdb_00001y7m

Crystal Structure of the B. subtilis YkuD protein at 2 A resolution

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)
A	d1y7ma1	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	Hypothetical protein YkuD, C-terminal domain	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
A	d1y7ma2	Alpha and beta proteins (a+b)	LysM domain	LysM domain	LysM domain	Hypothetical protein YkuD, N-terminal domain	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
B	d1y7mb1	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	Hypothetical protein YkuD, C-terminal domain	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)
B	d1y7mb2	Alpha and beta proteins (a+b)	LysM domain	LysM domain	LysM domain	Hypothetical protein YkuD, N-terminal domain	(Bacillus subtilis subsp. subtilis str. 168 ) [TaxId: 224308 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	L, D-transpeptidase catalytic domain-like	8021782	4002015	SCOP2 (2022-06-29)
A	SCOP2 Family	LysM domain	8021785	4000905	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	L, D-transpeptidase catalytic domain-like	8034162	3000695	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LysM domain-like	8034165	3001938	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	LysM domain-like	8034165	3001938	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	L, D-transpeptidase catalytic domain-like	8034162	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)
A	YkuD	e1y7mA1	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	LysM_1	e1y7mA2	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: LysM_1	ECOD (1.6)
B	YkuD	e1y7mB1	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	LysM_1	e1y7mB2	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: LysM_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.350.10	Alpha Beta	Roll	Membrane-bound Lytic Murein Transglycosylase D	Chain A	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)
B	3.10.350.10	Alpha Beta	Roll	Membrane-bound Lytic Murein Transglycosylase D	Chain A	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)

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
A, B	PF01476	LysM domain (LysM)	LysM domain	The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation [1]. This domain may have a general peptidoglycan binding function. The structure of this domain is known [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	hypothetical protein BSU14040	glycosyltransferase activity transferase activity catalytic activity 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 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 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 sporulation resulting in formation of a cellular spore anatomical structure formation involved in morphogenesis sporulation	cell periphery cellular anatomical structure external encapsulating structure cell wall spore wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR050979	Bacterial L,D-transpeptidase	Family
A, B	IPR036779	LysM domain superfamily	Homologous Superfamily
A, B	IPR018392	LysM domain	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.