5E27 | pdb_00005e27

The structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	RPF-like	8021037	4002498	SCOP2 (2022-06-29)
A	SCOP2 Family	RpfB N-terminal domain repeat-like	8045335	4004419	SCOP2 (2022-06-29)
A	SCOP2 Family	G5 domain-like	8090255	4007698	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Lysozyme-like	8033417	3001879	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MoaD/ThiS-like	8090254	3000330	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	G5 domain-like	8090256	3002424	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	G5 domain-like	8090256	3002424	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Lysozyme-like	8033417	3001879	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MoaD/ThiS-like	8090254	3000330	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	EF-hand_1, EF-hand_6, EF-hand_7	e5e27A1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: EF-hand_1, EF-hand_6, EF-hand_7	ECOD (v294.1)
A	G5	e5e27A2	A: a/b three-layered sandwiches	X: Arterivirus nucleocapsid protein	H: Arterivirus nucleocapsid protein	T: Arterivirus nucleocapsid protein	F: G5	ECOD (v294.1)
A	CoV_nucleocap	e5e27A3	A: a/b three-layered sandwiches	X: Arterivirus nucleocapsid protein	H: Arterivirus nucleocapsid protein	T: Arterivirus nucleocapsid protein	F: CoV_nucleocap	ECOD (v294.1)
B	HATPase_c	e5e27B2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: HATPase_c	ECOD (v294.1)
B	Thaumatin	e5e27B1	A: a/b three-layered sandwiches	X: Ntn/PP2C	H: Ntn	T: Penicillin acylase, catalytic domain	F: Thaumatin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.20.230.10	Mainly Beta	Single Sheet	Resuscitation-promoting factor rpfb fold	Resuscitation-promoting factor rpfb.	CATH (4.3.0)
A	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)
B	2.20.230.10	Mainly Beta	Single Sheet	Resuscitation-promoting factor rpfb fold	Resuscitation-promoting factor rpfb.	CATH (4.3.0)
B	1.10.530.10	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03990	G5-linked-Ubiquitin-like domain (DUF348)	G5-linked-Ubiquitin-like domain	This domain normally occurs as tandem repeats; however it is found as a single copy in the S. cerevisiae DNA-binding nuclear protein YCR593 (Swiss:P25357). This protein is involved in sporulation part of the SET3C complex, which is required to repres ...	This domain normally occurs as tandem repeats; however it is found as a single copy in the S. cerevisiae DNA-binding nuclear protein YCR593 (Swiss:P25357). This protein is involved in sporulation part of the SET3C complex, which is required to repress early/middle sporulation genes during meiosis ([2]). The bacterial proteins are likely to be involved in a cell wall function as they are found in conjunction with the Pfam:PF07501 domain, which is involved in various cell surface processes. This domain is also present in the resuscitation-promoting factors RpfB from Mycobacterium tuberculosis and Rpf2 from Corynebacterium glutamicum. These are factors that stimulate resuscitation of dormant cells [3]. This domain has a beta grasp fold. Structural description of this domain revealed a structural conservation between these domains and ubiquitin, hence it is termed UBL-G5 [4].	Domain
A, B	PF07501	G5 domain (G5)	G5 domain	This domain is found in a wide range of extracellular proteins. It is found tandemly repeated in up to 8 copies. It is found in the N-terminus of peptidases belonging to the M26 family which cleave human IgA. The domain is also found in proteins in ...	This domain is found in a wide range of extracellular proteins. It is found tandemly repeated in up to 8 copies. It is found in the N-terminus of peptidases belonging to the M26 family which cleave human IgA. The domain is also found in proteins involved in metabolism of bacterial cell walls suggesting this domain may have an adhesive function.	Domain
A, B	PF06737	Transglycosylase-like domain (Transglycosylas)	Transglycosylase-like domain	This family of proteins are very likely to act as transglycosylase enzymes related to Pfam:PF00062 and Pfam:PF01464. These other families are weakly matched by this family, and include the known active site residues.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Resuscitation-promoting factor RpfB	hydrolase activity catalytic activity	regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process response to stimulus signaling quorum sensing cell-cell signaling detection of cell density detection of biotic stimulus response to biotic stimulus cell communication detection of stimulus cell population proliferation regulation of cell population proliferation developmental process biological process involved in interspecies interaction between organisms dormancy exit of symbiont in host formation of structure involved in a symbiotic process development of symbiont in host dormancy process negative regulation of metabolic process negative regulation of biological process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of cellular process negative regulation of macromolecule metabolic process	cellular anatomical structure extracellular region cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR010618	Resuscitation-promoting factor, core lysozyme-like domain	Domain
A, B	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
A, B	IPR011098	G5 domain	Domain
A, B	IPR007137	Resuscitation-promoting factor, domain of unknown function DUF348	Domain
A, B	IPR051933	Bacterial Resuscitation-promoting factor RpfB	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.