3HMB | pdb_00003hmb

Mutant endolysin from Bacillus 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)
A	d3hmba_	Alpha and beta proteins (a+b)	N-acetylmuramoyl-L-alanine amidase-like	N-acetylmuramoyl-L-alanine amidase-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d3hmbb1	Alpha and beta proteins (a+b)	N-acetylmuramoyl-L-alanine amidase-like	N-acetylmuramoyl-L-alanine amidase-like	automated matches	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d3hmbb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d3hmbc_	Alpha and beta proteins (a+b)	N-acetylmuramoyl-L-alanine amidase-like	N-acetylmuramoyl-L-alanine amidase-like	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)
A	SCOP2 Family	N-acetylmuramoyl-L-alanine amidase-like	8058648	4001915	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	N-acetylmuramoyl-L-alanine amidase-like	8058649	3000555	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	N-acetylmuramoyl-L-alanine amidase-like	8058649	3000555	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	N-acetylmuramoyl-L-alanine amidase-like	8058649	3000555	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	Thymidylat_synt	e3hmbA1	A: alpha bundles	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Thymidylat_synt	ECOD (develop294)
B	Thymidylat_synt	e3hmbB1	A: alpha bundles	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Thymidylat_synt	ECOD (develop294)
C	Thymidylat_synt	e3hmbC1	A: alpha bundles	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Thymidylat_synt	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.80.10	Alpha Beta	3-Layer(aba) Sandwich	Lysozyme-like	Peptidoglycan recognition protein-like	CATH (4.3.0)
B	3.40.80.10	Alpha Beta	3-Layer(aba) Sandwich	Lysozyme-like	Peptidoglycan recognition protein-like	CATH (4.3.0)
C	3.40.80.10	Alpha Beta	3-Layer(aba) Sandwich	Lysozyme-like	Peptidoglycan recognition protein-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01510	N-acetylmuramoyl-L-alanine amidase (Amidase_2)	N-acetylmuramoyl-L-alanine amidase	This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala). The ...	This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala). The structure is known for the bacteriophage T7 structure and shows that two of the conserved histidines are zinc binding.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	N-acetylmuramoyl-L-alanine amidase xlyA	peptidoglycan muralytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity catalytic activity N-acetylmuramoyl-L-alanine amidase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	DNA-mediated transformation cellular response to stimulus horizontal gene transfer response to stimulus establishment of competence for transformation cellular process cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization sporulation resulting in formation of a cellular spore developmental process anatomical structure morphogenesis DNA-mediated transformation cellular response to stimulus horizontal gene transfer response to stimulus establishment of competence for transformation cellular process cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization sporulation resulting in formation of a cellular spore developmental process anatomical structure morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development sporulation carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process macromolecule metabolic process peptidoglycan turnover	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR002477	Peptidoglycan binding-like	Domain
A, B, C	IPR036365	PGBD-like superfamily	Homologous Superfamily
A, B, C	IPR002502	N-acetylmuramoyl-L-alanine amidase domain	Domain
A, B, C	IPR036779	LysM domain superfamily	Homologous Superfamily
A, B, C	IPR036505	N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily	Homologous Superfamily
A, B, C	IPR036366	PGBD superfamily	Homologous Superfamily
A, B, C	IPR018392	LysM domain	Domain
A, B, C	IPR051206	N-acetylmuramoyl-L-alanine amidase 2	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.