2DLN | pdb_00002dln

VANCOMYCIN RESISTANCE: STRUCTURE OF D-ALANINE:D-ALANINE LIGASE AT 2.3 ANGSTROMS 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
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	d2dlna1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	D-Alanine ligase N-terminal domain	D-Ala-D-Ala ligase, N-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2dlna2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	ATP-binding domain of peptide synthetases	D-ala-D-ala ligase, C-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8036516	3000094	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PreATP-grasp domain	8044233	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	LRR_6,LRR_RI_capping	e2dlnA1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: LRR_6,LRR_RI_capping	ECOD (develop294)
A	GBP	e2dlnA2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: GBP	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
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)

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	D-ALANINE--D-ALANINE LIGASE	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 identical protein binding protein binding protein homodimerization activity protein dimerization 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 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 cell wall macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

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

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

Chains	Enzyme Name	Description	Catalytic Residues
A	D-alanine---D-alanine ligase M-CSA #883	D-alanine--D-alanine ligase (EC:6.3.2.4) is a bacterial enzyme involved in cell-wall biosynthesis. It participates in forming UDP-N-acetylmuramoyl pentapeptide, the peptidoglycan precursor.	Defined by 8 residues: GLU:A-15SER:A-150TYR:A-216ARG:A-255ASP:A-257GLU:A-270ASN:A-272GLY:A-276 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 6.3.2.4 (PDB Primary Data) Search M-CSA Motif + EC 6.3.2.4

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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