8XUD | pdb_00008xud

Crystal structure of adaptor NlpI in complex with endopeptidase MepS and PDZ-protease Prc

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	TPR-like	8044044	3001345	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TPR-like	8044044	3001345	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth I], F [auth J], G [auth K], H [auth L]	PF00877	NlpC/P60 family (NLPC_P60)	NlpC/P60 family	The function of this domain is unknown. It is found in several lipoproteins.	Domain
C, D	PF17804	Tail specific protease N-terminal domain (TSP_NTD)	Tail specific protease N-terminal domain	The N-terminal domain of tail specific proteases has a novel fold composed of 10 alpha helices [1].	Domain
C, D	PF03572	Peptidase family S41 (Peptidase_S41)	Peptidase family S41	-	Family
C, D	PF11818	C-terminal domain of tail specific protease (DUF3340) (DUF3340)	C-terminal domain of tail specific protease (DUF3340)	-	Family
C, D	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
J [auth N]	Substrate peptide	-	-	-
I [auth M]	Substrate peptide	-	-	-
E [auth I], F [auth J], G [auth K], H [auth L]	Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase	peptidase activity catalytic activity, acting on a protein muramoyltetrapeptide carboxypeptidase activity hydrolase activity exopeptidase activity catalytic activity carboxypeptidase activity cysteine-type peptidase activity endopeptidase activity	glycosaminoglycan metabolic process aminoglycan metabolic process peptidoglycan metabolic process carbohydrate derivative metabolic process metabolic process cellular process macromolecule metabolic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process primary metabolic process macromolecule biosynthetic process cellular component organization capsule organization glycosaminoglycan metabolic process aminoglycan metabolic process peptidoglycan metabolic process carbohydrate derivative metabolic process metabolic process cellular process macromolecule metabolic process carbohydrate metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process primary metabolic process macromolecule biosynthetic process cellular component organization capsule organization polysaccharide metabolic process biosynthetic process cellular component organization or biogenesis capsule polysaccharide biosynthetic process external encapsulating structure organization proteolysis protein metabolic process cell wall organization or biogenesis cell wall organization peptidoglycan turnover	cell periphery cell outer membrane cellular anatomical structure external encapsulating structure membrane cell envelope outer membrane
C, D	Tail-specific protease	peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity	symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated evasion of recognition by host innate immune effector symbiont-mediated response to host defenses symbiont-mediated evasion of host innate immune response response to external stimulus biological process involved in interaction with host response to biotic stimulus biological process involved in symbiotic interaction symbiont-mediated evasion of recognition by host complement symbiont-mediated perturbation of host process response to host immune response symbiont-mediated perturbation of host defense response biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host immune response symbiont-mediated evasion of recognition by host innate immune effector symbiont-mediated response to host defenses symbiont-mediated evasion of host innate immune response response to external stimulus biological process involved in interaction with host response to biotic stimulus biological process involved in symbiotic interaction symbiont-mediated evasion of recognition by host complement symbiont-mediated perturbation of host process response to host immune response symbiont-mediated evasion of host immune response response to host response to external biotic stimulus modulation of process of another organism response to chemical response to antibiotic catabolic process metabolic process cellular process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process proteolysis cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation signal transduction cell communication	cell periphery cellular anatomical structure plasma membrane membrane outer membrane-bounded periplasmic space cell envelope periplasmic space
A, B	Lipoprotein NlpI	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity protein-macromolecule adaptor activity molecular adaptor activity	glycosaminoglycan metabolic process aminoglycan metabolic process peptidoglycan metabolic process carbohydrate derivative metabolic process metabolic process cellular process macromolecule metabolic process cell division	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth I], F [auth J], G [auth K], H [auth L]	IPR052062	Murein DD-endopeptidase/LD-carboxypeptidase	Family
E [auth I], F [auth J], G [auth K], H [auth L]	IPR000064	Endopeptidase, NLPC/P60 domain	Domain
E [auth I], F [auth J], G [auth K], H [auth L]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
C, D	IPR040573	Tail specific protease, N-terminal domain	Domain
C, D	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
C, D	IPR020992	Tail specific protease, C-terminal	Domain
C, D	IPR036034	PDZ superfamily	Homologous Superfamily
C, D	IPR005151	Tail specific protease	Domain
C, D	IPR001478	PDZ domain	Domain
C, D	IPR004447	C-terminal-processing peptidase S41A	Family
A, B	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A, B	IPR050498	Photosystem I assembly protein Ycf3	Family
A, B	IPR019734	Tetratricopeptide repeat	Repeat
A, B	IPR023605	Lipoprotein NlpI	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.