1E4E | pdb_00001e4e

D-alanyl-D-lacate ligase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
AMR Gene: CARD Annotation
AMR Gene Family: CARD Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1e4ea1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	D-Alanine ligase N-terminal domain	D-alanine:D-lactate ligase VanA, N-domain	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)
A	d1e4ea2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	ATP-binding domain of peptide synthetases	D-alanine:D-lactate ligase VanA, C-domain	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)
B	d1e4eb1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	D-Alanine ligase N-terminal domain	D-alanine:D-lactate ligase VanA, N-domain	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)
B	d1e4eb2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	ATP-binding domain of peptide synthetases	D-alanine:D-lactate ligase VanA, C-domain	(Enterococcus faecium ) [TaxId: 1352 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	D-Alanine ligase N-terminal domain	8020155	4003870	SCOP2 (2022-06-29)
A	SCOP2 Family	ATP-binding domain of peptide synthetases	8020158	4002041	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PreATP-grasp domain	8032535	3001680	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glutathione synthetase ATP-binding domain-like	8032538	3000094	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8032538	3000094	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PreATP-grasp domain	8032535	3001680	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	ATP-grasp	e1e4eA1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
A	Dala_Dala_lig_N	e1e4eA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Dala_Dala_lig_N	ECOD (1.6)
B	ATP-grasp	e1e4eB1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
B	Dala_Dala_lig_N	e1e4eB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Dala_Dala_lig_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
A	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
B	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
B	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A	ARO:3000010	vanA	VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance.	CARD (4.0.0)
A	ARO:3000010	vanA	VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance.	CARD (4.0.0)
B	ARO:3000010	vanA	VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance.	CARD (4.0.0)
B	ARO:3000010	vanA	VanA is a D-Ala-D-Ala ligase homolog that synthesizes D-Ala-D-Lac, an alternative substrate for peptidoglycan synthesis that reduces vancomycin binding affinity. It has been isolated from VREs. It is associated with both vancomycin and teicoplanin resistance.	CARD (4.0.0)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A	ARO:3002906	Van ligase	glycopeptide antibiotic	antibiotic target alteration	CARD (4.0.0)
A	ARO:3002906	Van ligase	glycopeptide antibiotic	antibiotic target alteration	CARD (4.0.0)
B	ARO:3002906	Van ligase	glycopeptide antibiotic	antibiotic target alteration	CARD (4.0.0)
B	ARO:3002906	Van ligase	glycopeptide antibiotic	antibiotic target alteration	CARD (4.0.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07478	D-ala D-ala ligase C-terminus (Dala_Dala_lig_C)	D-ala D-ala ligase C-terminus	-	Family
A	PF01820	D-ala D-ala ligase N-terminus (Dala_Dala_lig_N)	D-ala D-ala ligase N-terminus	-	Family
B	PF07478	D-ala D-ala ligase C-terminus (Dala_Dala_lig_C)	D-ala D-ala ligase C-terminus	-	Family
B	PF01820	D-ala D-ala ligase N-terminus (Dala_Dala_lig_N)	D-ala D-ala ligase N-terminus	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding acid-amino acid ligase activity D-alanine-D-alanine ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity cation binding metal ion 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 cellular component organization cell wall organization or biogenesis cell wall organization 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 component organization cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization response to stimulus response to chemical response to antibiotic carbohydrate derivative biosynthetic process peptidoglycan-based cell wall 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 metabolic process glycosaminoglycan biosynthetic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane
B	VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding acid-amino acid ligase activity D-alanine-D-alanine ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity cation binding metal ion 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 cellular component organization cell wall organization or biogenesis cell wall organization 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 component organization cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis external encapsulating structure organization response to stimulus response to chemical response to antibiotic carbohydrate derivative biosynthetic process peptidoglycan-based cell wall 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 metabolic process glycosaminoglycan biosynthetic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR011761	ATP-grasp fold	Domain
A	IPR011095	D-alanine--D-alanine ligase, C-terminal	Domain
A	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A	IPR000291	D-alanine--D-alanine ligase/VANA/B/C, conserved site	Conserved Site
A	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
A	IPR005905	D-alanine--D-alanine ligase	Family
A	IPR011127	D-alanine--D-alanine ligase, N-terminal domain	Domain
B	IPR011761	ATP-grasp fold	Domain
B	IPR011095	D-alanine--D-alanine ligase, C-terminal	Domain
B	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
B	IPR000291	D-alanine--D-alanine ligase/VANA/B/C, conserved site	Conserved Site
B	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
B	IPR005905	D-alanine--D-alanine ligase	Family
B	IPR011127	D-alanine--D-alanine ligase, N-terminal domain	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	D-alanine-(R)-lactate ligase M-CSA #310	D-alanine--D-alanine ligase (EC:6.3.2.4) is a bacterial enzyme involved in cell-wall biosynthesis. The product of this enzyme, the depsipeptide D-alanyl-(R)-lactate, can be incorporated into the peptidoglycan pentapeptide instead of the usual D-alanyl-D-alanine dipeptide. The resulting peptidoglycan does not bind the glycopeptide antibiotics vancomycin and teicoplanin, conferring resistance on the bacteria.	Defined by 8 residues: VAL:A-19LYS:A-22HIS:A-99HIS:A-244GLU:A-250ARG:A-290GLY:A-311TYR:A-315 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 6.1.2.1 (PDB Primary Data) Search M-CSA Motif + EC 6.1.2.1

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.