7NPT

Cytosolic bridge of an intact ESX-5 inner membrane complex

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth D7]	YukD	e7nptD71	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: YukD	ECOD (1.6)
C [auth D8]	YukD	e7nptD81	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: YukD	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth D7], C [auth D8]	PF19053	EccD-like transmembrane domain (EccD)	EccD-like transmembrane domain	-	Family
B [auth D7], C [auth D8]	PF08817	WXG100 protein secretion system (Wss), protein YukD (YukD)	WXG100 protein secretion system (Wss), protein YukD	The YukD protein family members participate in the formation of a translocon required for the secretion of WXG100 proteins (Pfam:PF06013) in monoderm bacteria, with the WXG100 protein secretion system (Wss). Like the cytoplasmic protein EsaC in Staph ...	The YukD protein family members participate in the formation of a translocon required for the secretion of WXG100 proteins (Pfam:PF06013) in monoderm bacteria, with the WXG100 protein secretion system (Wss). Like the cytoplasmic protein EsaC in Staphylococcus aureus, YukD was hypothesized to play a role of a chaperone. YukD adopts a ubiquitin-like fold [1]. Usually, ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that the classical YukD lacks the capacity for covalent bond formation with other proteins [1]. In contrast to the situation in firmicutes, YukD-like proteins in actinobacteria are often fused to a transporter involved in the ESAT-6/ESX/Wss secretion pathway [6,7]. Members of the YukD family are also associated in gene neighborhoods with other enzymatic members of the ubiquitin signaling and degradation pathway such as the E1, E2 and E3 trienzyme complex that catalyze ubiquitin transfer to substrates, and the JAB family metallopeptidases that are involved in its release [7]. This suggests that a subset of the YukD family in bacteria are conjugated and released from proteins as in the eukaryotic ubiquitin-mediated signaling and degradation pathway [7].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C1]	ESX-5 secretion system protein EccC5	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity	-	cell periphery plasma membrane membrane cellular anatomical entity external encapsulating structure cell wall peptidoglycan-based cell wall
B [auth D7], C [auth D8]	ESX-5 secretion system protein EccD5	-	-	cell periphery plasma membrane membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C1]	IPR002543	FtsK domain	Domain
A [auth C1]	IPR003593	AAA+ ATPase domain	Domain
A [auth C1]	IPR050206	FtsK/SpoIIIE/SftA cell division and DNA translocation	Family
A [auth C1]	IPR023837	EccCb-like, Actinobacteria	Family
A [auth C1]	IPR023836	EccCa-like, Actinobacteria	Family
A [auth C1]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth D7], C [auth D8]	IPR044049	EccD-like transmembrane domain	Domain
B [auth D7], C [auth D8]	IPR006707	Type VII secretion system membrane protein EccD	Family
B [auth D7], C [auth D8]	IPR024962	YukD-like	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 R01GM133198.