Annotations: 4Y4V

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	YkuD	e4y4vA1	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	YafK_like	e4y4vA3	A: alpha arrays	X: Cell-shape determining Csd6 N-terminal dimerization domain (From Topology)	H: Cell-shape determining Csd6 N-terminal dimerization domain (From Topology)	T: Cell-shape determining Csd6 N-terminal dimerization domain	F: YafK_like	ECOD (1.6)
A	DUF4440	e4y4vA2	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: DUF4440	ECOD (1.6)
B	YkuD	e4y4vB1	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	YafK_like	e4y4vB3	A: alpha arrays	X: Cell-shape determining Csd6 N-terminal dimerization domain (From Topology)	H: Cell-shape determining Csd6 N-terminal dimerization domain (From Topology)	T: Cell-shape determining Csd6 N-terminal dimerization domain	F: YafK_like	ECOD (1.6)
B	DUF4440	e4y4vB2	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: DUF4440	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22401	Cell-shape determining Csd6 N-terminal dimerization domain (Csd6-like_dimeriz)	Cell-shape determining Csd6 N-terminal dimerization domain	This entry represents the dimerization domain found at the N-terminal of Cds6 from H. pylori, a cell shape-determining protein that plays key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. It is also involved in de ...	This entry represents the dimerization domain found at the N-terminal of Cds6 from H. pylori, a cell shape-determining protein that plays key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. It is also involved in deglycosylation of the flagellar protein FlaA [1].	Domain
A	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
B	PF22401	Cell-shape determining Csd6 N-terminal dimerization domain (Csd6-like_dimeriz)	Cell-shape determining Csd6 N-terminal dimerization domain	This entry represents the dimerization domain found at the N-terminal of Cds6 from H. pylori, a cell shape-determining protein that plays key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. It is also involved in de ...	This entry represents the dimerization domain found at the N-terminal of Cds6 from H. pylori, a cell shape-determining protein that plays key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. It is also involved in deglycosylation of the flagellar protein FlaA [1].	Domain
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	Conserved hypothetical secreted protein	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 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 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	-
B	Conserved hypothetical secreted protein	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 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 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	IPR032710	NTF2-like domain superfamily	Homologous Superfamily
A	IPR054516	Cell-shape determining Csd6, N-terminal dimerization domain	Domain
A	IPR005490	L,D-transpeptidase catalytic domain	Domain
A	IPR038063	L,D-transpeptidase catalytic domain-like	Homologous Superfamily
B	IPR032710	NTF2-like domain superfamily	Homologous Superfamily
B	IPR054516	Cell-shape determining Csd6, N-terminal dimerization domain	Domain
B	IPR005490	L,D-transpeptidase catalytic domain	Domain
B	IPR038063	L,D-transpeptidase catalytic domain-like	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210

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.