4A1I

ykud from B.subtilis

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)
B	d4a1ib2	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d4a1ib1	Alpha and beta proteins (a+b)	LysM domain	LysM domain	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d4a1ib3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
H	d4a1ih2	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
H	d4a1ih1	Alpha and beta proteins (a+b)	LysM domain	LysM domain	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d4a1ia2	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d4a1ia1	Alpha and beta proteins (a+b)	LysM domain	LysM domain	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d4a1ia3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d4a1ic2	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d4a1ic1	Alpha and beta proteins (a+b)	LysM domain	LysM domain	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d4a1ic3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d4a1id2	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d4a1id1	Alpha and beta proteins (a+b)	LysM domain	LysM domain	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d4a1id3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d4a1ie2	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d4a1ie1	Alpha and beta proteins (a+b)	LysM domain	LysM domain	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d4a1if2	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d4a1if1	Alpha and beta proteins (a+b)	LysM domain	LysM domain	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
G	d4a1ig2	All beta proteins	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	L,D-transpeptidase catalytic domain-like	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
G	d4a1ig1	Alpha and beta proteins (a+b)	LysM domain	LysM domain	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
H	SCOP2B Superfamily	LysM domain-like	8034165	3001938	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	L D-transpeptidase catalytic domain-like	8034162	3000695	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	L D-transpeptidase catalytic domain-like	8034162	3000695	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	LysM domain-like	8034165	3001938	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	L D-transpeptidase catalytic domain-like	8034162	3000695	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	LysM domain-like	8034165	3001938	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	L D-transpeptidase catalytic domain-like	8034162	3000695	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	LysM domain-like	8034165	3001938	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	L D-transpeptidase catalytic domain-like	8034162	3000695	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	LysM domain-like	8034165	3001938	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	L D-transpeptidase catalytic domain-like	8034162	3000695	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	LysM domain-like	8034165	3001938	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	LysM domain-like	8034165	3001938	SCOP2B (2022-06-29)
G	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)
B	PF03734	e4a1iB1	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: PF03734	ECOD (1.6)
B	PF01476	e4a1iB2	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: PF01476	ECOD (1.6)
H	PF03734	e4a1iH1	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: PF03734	ECOD (1.6)
H	PF01476	e4a1iH2	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: PF01476	ECOD (1.6)
A	PF03734	e4a1iA1	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: PF03734	ECOD (1.6)
A	PF01476	e4a1iA2	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: PF01476	ECOD (1.6)
C	PF03734	e4a1iC1	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: PF03734	ECOD (1.6)
C	PF01476	e4a1iC2	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: PF01476	ECOD (1.6)
D	PF03734	e4a1iD1	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: PF03734	ECOD (1.6)
D	PF01476	e4a1iD2	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: PF01476	ECOD (1.6)
E	PF03734	e4a1iE1	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: PF03734	ECOD (1.6)
E	PF01476	e4a1iE2	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: PF01476	ECOD (1.6)
F	PF03734	e4a1iF1	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: PF03734	ECOD (1.6)
F	PF01476	e4a1iF2	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: PF01476	ECOD (1.6)
G	PF03734	e4a1iG1	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: PF03734	ECOD (1.6)
G	PF01476	e4a1iG2	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: PF01476	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
H	3.10.350.10	Alpha Beta	Roll	Membrane-bound Lytic Murein Transglycosylase D	Chain A	CATH (4.3.0)
H	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	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)
C	3.10.350.10	Alpha Beta	Roll	Membrane-bound Lytic Murein Transglycosylase D	Chain A	CATH (4.3.0)
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)
D	3.10.350.10	Alpha Beta	Roll	Membrane-bound Lytic Murein Transglycosylase D	Chain A	CATH (4.3.0)
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)
E	3.10.350.10	Alpha Beta	Roll	Membrane-bound Lytic Murein Transglycosylase D	Chain A	CATH (4.3.0)
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)
F	3.10.350.10	Alpha Beta	Roll	Membrane-bound Lytic Murein Transglycosylase D	Chain A	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)
G	3.10.350.10	Alpha Beta	Roll	Membrane-bound Lytic Murein Transglycosylase D	Chain A	CATH (4.3.0)
G	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, C, D, E A, B, C, D, E, F, G, H	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, C, D, E A, B, C, D, E, F, G, H	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, C, D, E A, B, C, D, E, F, G, H	PUTATIVE L, D-TRANSPEPTIDASE YKUD	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 cellular biosynthetic process cell wall organization or biogenesis glycosaminoglycan metabolic 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 cellular biosynthetic process cell wall organization or biogenesis glycosaminoglycan metabolic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process cellular component biogenesis peptidoglycan-protein cross-linking organic substance metabolic process peptidoglycan metabolic process organic substance biosynthetic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis organonitrogen compound metabolic process cellular metabolic process macromolecule biosynthetic process peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process aminoglycan biosynthetic process cellular process metabolic process 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	extracellular region cellular anatomical entity cell periphery external encapsulating structure cell wall spore wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036779	LysM domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018392	LysM domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR005490	L,D-transpeptidase catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR038063	L,D-transpeptidase catalytic domain-like	Homologous Superfamily

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4A1I

ykud from B.subtilis

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage