1W79 | pdb_00001w79

Crystal structure of the DD-transpeptidase-carboxypeptidase from Actinomadura R39

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d1w79d1	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Dac-like	D-alanyl-D-alanine carboxypeptidase Dac	(Actinomadura sp. R39 ) [TaxId: 72570 ],	SCOPe (2.08)
C	d1w79c1	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Dac-like	D-alanyl-D-alanine carboxypeptidase Dac	(Actinomadura sp. R39 ) [TaxId: 72570 ],	SCOPe (2.08)
B	d1w79b1	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Dac-like	D-alanyl-D-alanine carboxypeptidase Dac	(Actinomadura sp. R39 ) [TaxId: 72570 ],	SCOPe (2.08)
A	d1w79a1	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	Dac-like	D-alanyl-D-alanine carboxypeptidase Dac	(Actinomadura sp. R39 ) [TaxId: 72570 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8032917	3001604	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8032917	3001604	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8032917	3001604	SCOP2B (2022-06-29)
A	SCOP2 Family	Dac-like	8020537	4000441	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	beta-lactamase/transpeptidase-like	8032917	3001604	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	PABP	e1w79D1	A: alpha bundles	X: EGF-like	H: PABC(PABP) domain	T: PABC(PABP) domain	F: PABP	ECOD (develop294)
D	Ion_trans_2	e1w79D2	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Ion_trans_2	ECOD (develop294)
D	NIR_SIR	e1w79D3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: NIR_SIR	ECOD (develop294)
D	Glyco_hydro_20b	e1w79D4	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Glyco_hydro_20b	ECOD (develop294)
C	PABP	e1w79C1	A: alpha bundles	X: EGF-like	H: PABC(PABP) domain	T: PABC(PABP) domain	F: PABP	ECOD (develop294)
C	Ion_trans_2	e1w79C2	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Ion_trans_2	ECOD (develop294)
C	NIR_SIR	e1w79C3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: NIR_SIR	ECOD (develop294)
C	Glyco_hydro_20b	e1w79C4	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Glyco_hydro_20b	ECOD (develop294)
B	PABP	e1w79B1	A: alpha bundles	X: EGF-like	H: PABC(PABP) domain	T: PABC(PABP) domain	F: PABP	ECOD (develop294)
B	Ion_trans_2	e1w79B2	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Ion_trans_2	ECOD (develop294)
B	NIR_SIR	e1w79B3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: NIR_SIR	ECOD (develop294)
B	Glyco_hydro_20b	e1w79B4	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Glyco_hydro_20b	ECOD (develop294)
A	Peptidase_S13	e1w79A1	A: beta complex topology	X: Inserted beta sandwich domain in Dac-like proteins	H: Inserted beta sandwich domain in Dac-like proteins	T: Inserted beta sandwich domain in Dac-like proteins	F: Peptidase_S13	ECOD (develop294)
A	Peptidase_S13	e1w79A2	A: a+b two layers	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Peptidase_S13	ECOD (develop294)
A	Peptidase_S13	e1w79A3	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Peptidase_S13	ECOD (develop294)
A	Peptidase_S13	e1w79A4	A: alpha bundles	X: DTD-like	H: Inserted a+b domain in Dac-like proteins	T: Inserted a+b domain in Dac-like proteins	F: Peptidase_S13	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
D	3.50.80.20	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
C	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
C	3.50.80.20	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
B	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
B	3.50.80.20	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)
A	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
A	3.50.80.20	Alpha Beta	3-Layer(bba) Sandwich	D-tyrosyl-trna(Tyr) Deacylase	Chain: A	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	D-alanyl-D-alanine carboxypeptidase	serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity hydrolase activity serine-type D-Ala-D-Ala carboxypeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity exopeptidase activity catalytic 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 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 cell wall macromolecule metabolic process proteolysis primary metabolic process protein metabolic process cellular component organization cell wall organization external encapsulating structure organization response to stimulus response to chemical response to antibiotic	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B, C, D	IPR000667	Peptidase S13, D-Ala-D-Ala carboxypeptidase C	Family

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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