4O4U | pdb_00004o4u

Crystal structure of the vaccine antigen Transferrin Binding Protein B (TbpB) mutant Trp-176-Ala from Haemophilus parasuis Hp5

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	d4o4ua1	All beta proteins	Handle domain of Transferrin binding protein TbpB-like	Handle domain of Transferrin binding protein TbpB-like	automated matches	automated matches	(Glaesserella parasuis ) [TaxId: 738 ],	SCOPe (2.08)
A	d4o4ua2	Membrane and cell surface proteins and peptides	Transmembrane beta-barrels	OMPA-like	automated matches	automated matches	(Glaesserella parasuis ) [TaxId: 738 ],	SCOPe (2.08)
B	d4o4ub1	All beta proteins	Handle domain of Transferrin binding protein TbpB-like	Handle domain of Transferrin binding protein TbpB-like	automated matches	automated matches	(Glaesserella parasuis ) [TaxId: 738 ],	SCOPe (2.08)
B	d4o4ub2	Membrane and cell surface proteins and peptides	Transmembrane beta-barrels	OMPA-like	automated matches	automated matches	(Glaesserella parasuis ) [TaxId: 738 ],	SCOPe (2.08)
C	d4o4uc1	All beta proteins	Handle domain of Transferrin binding protein TbpB-like	Handle domain of Transferrin binding protein TbpB-like	automated matches	automated matches	(Glaesserella parasuis ) [TaxId: 738 ],	SCOPe (2.08)
C	d4o4uc2	Membrane and cell surface proteins and peptides	Transmembrane beta-barrels	OMPA-like	automated matches	automated matches	(Glaesserella parasuis ) [TaxId: 738 ],	SCOPe (2.08)
D	d4o4ud1	All beta proteins	Handle domain of Transferrin binding protein TbpB-like	Handle domain of Transferrin binding protein TbpB-like	automated matches	automated matches	(Glaesserella parasuis ) [TaxId: 738 ],	SCOPe (2.08)
D	d4o4ud2	Membrane and cell surface proteins and peptides	Transmembrane beta-barrels	OMPA-like	automated matches	automated matches	(Glaesserella parasuis ) [TaxId: 738 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	TbpB N-lobe and C-lobe handle domains-like	8052212	3002099	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TbpB N-lobe and C-lobe handle domains-like	8052213	3002099	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TbpB N-lobe and C-lobe beta-barrel domains-like	8052211	3002098	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TbpB N-lobe and C-lobe beta-barrel domains-like	8047027	3002098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TbpB N-lobe and C-lobe handle domains-like	8052212	3002099	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TbpB N-lobe and C-lobe handle domains-like	8052213	3002099	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TbpB N-lobe and C-lobe beta-barrel domains-like	8047027	3002098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TbpB N-lobe and C-lobe beta-barrel domains-like	8052211	3002098	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TbpB N-lobe and C-lobe beta-barrel domains-like	8047027	3002098	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TbpB N-lobe and C-lobe handle domains-like	8052213	3002099	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TbpB N-lobe and C-lobe handle domains-like	8052212	3002099	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TbpB N-lobe and C-lobe beta-barrel domains-like	8052211	3002098	SCOP2B (2022-06-29)
D	SCOP2 Family	N-lobe and C-lobe of Tf-binding protein B-like	8047018	4006246	SCOP2 (2022-06-29)
D	SCOP2 Family	N-lobe and C-lobe of Tf-binding protein B-like	8048879	4006246	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	TbpB N-lobe and C-lobe beta-barrel domains-like	8052211	3002098	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	TbpB N-lobe and C-lobe beta-barrel domains-like	8047027	3002098	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	TbpB N-lobe and C-lobe handle domains-like	8052212	3002099	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	TbpB N-lobe and C-lobe handle domains-like	8052213	3002099	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)
A	TbpB_C	e4o4uA2	A: beta barrels	X: Handle domain in transferrin-binding protein B (From Topology)	H: Handle domain in transferrin-binding protein B (From Topology)	T: Handle domain in transferrin-binding protein B	F: TbpB_C	ECOD (1.6)
A	TbpB_A	e4o4uA4	A: beta barrels	X: Handle domain in transferrin-binding protein B (From Topology)	H: Handle domain in transferrin-binding protein B (From Topology)	T: Handle domain in transferrin-binding protein B	F: TbpB_A	ECOD (1.6)
A	TbpB_B_D	e4o4uA1	A: beta barrels	X: Outer membrane meander beta-barrels	H: OMPA-like (From Topology)	T: OMPA-like	F: TbpB_B_D	ECOD (1.6)
B	TbpB_C	e4o4uB1	A: beta barrels	X: Handle domain in transferrin-binding protein B (From Topology)	H: Handle domain in transferrin-binding protein B (From Topology)	T: Handle domain in transferrin-binding protein B	F: TbpB_C	ECOD (1.6)
B	TbpB_A	e4o4uB4	A: beta barrels	X: Handle domain in transferrin-binding protein B (From Topology)	H: Handle domain in transferrin-binding protein B (From Topology)	T: Handle domain in transferrin-binding protein B	F: TbpB_A	ECOD (1.6)
B	TbpB_B_D	e4o4uB3	A: beta barrels	X: Outer membrane meander beta-barrels	H: OMPA-like (From Topology)	T: OMPA-like	F: TbpB_B_D	ECOD (1.6)
C	TbpB_C	e4o4uC1	A: beta barrels	X: Handle domain in transferrin-binding protein B (From Topology)	H: Handle domain in transferrin-binding protein B (From Topology)	T: Handle domain in transferrin-binding protein B	F: TbpB_C	ECOD (1.6)
C	TbpB_A	e4o4uC3	A: beta barrels	X: Handle domain in transferrin-binding protein B (From Topology)	H: Handle domain in transferrin-binding protein B (From Topology)	T: Handle domain in transferrin-binding protein B	F: TbpB_A	ECOD (1.6)
C	TbpB_B_D	e4o4uC2	A: beta barrels	X: Outer membrane meander beta-barrels	H: OMPA-like (From Topology)	T: OMPA-like	F: TbpB_B_D	ECOD (1.6)
D	TbpB_C	e4o4uD2	A: beta barrels	X: Handle domain in transferrin-binding protein B (From Topology)	H: Handle domain in transferrin-binding protein B (From Topology)	T: Handle domain in transferrin-binding protein B	F: TbpB_C	ECOD (1.6)
D	TbpB_A	e4o4uD4	A: beta barrels	X: Handle domain in transferrin-binding protein B (From Topology)	H: Handle domain in transferrin-binding protein B (From Topology)	T: Handle domain in transferrin-binding protein B	F: TbpB_A	ECOD (1.6)
D	TbpB_B_D	e4o4uD3	A: beta barrels	X: Outer membrane meander beta-barrels	H: OMPA-like (From Topology)	T: OMPA-like	F: TbpB_B_D	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.128.250	Mainly Beta	Beta Barrel	Lipocalin		CATH (4.3.0)
A	2.40.160.90	Mainly Beta	Beta Barrel	Porin		CATH (4.3.0)
A	2.40.128.240	Mainly Beta	Beta Barrel	Lipocalin		CATH (4.3.0)
B	2.40.128.250	Mainly Beta	Beta Barrel	Lipocalin		CATH (4.3.0)
B	2.40.160.90	Mainly Beta	Beta Barrel	Porin		CATH (4.3.0)
B	2.40.128.240	Mainly Beta	Beta Barrel	Lipocalin		CATH (4.3.0)
C	2.40.128.250	Mainly Beta	Beta Barrel	Lipocalin		CATH (4.3.0)
C	2.40.160.90	Mainly Beta	Beta Barrel	Porin		CATH (4.3.0)
C	2.40.128.240	Mainly Beta	Beta Barrel	Lipocalin		CATH (4.3.0)
D	2.40.128.250	Mainly Beta	Beta Barrel	Lipocalin		CATH (4.3.0)
D	2.40.160.90	Mainly Beta	Beta Barrel	Porin		CATH (4.3.0)
D	2.40.128.240	Mainly Beta	Beta Barrel	Lipocalin		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF17483	C-lobe handle domain of Tf-binding protein B (TbpB_C)	C-lobe handle domain of Tf-binding protein B	Bacterial lipoproteins represent a large group of specialised membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis ...	Bacterial lipoproteins represent a large group of specialised membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence [1]. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialised uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf). TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a 'handle' domain made up of four (N lobe) or eight (C lobe) beta strands [2]. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf [3]. This domain family is found in the handle domain of the C lobe (domain C) of TbpB proteins. It consists of a squashed six-stranded beta sheet flanked by two antiparallel beta strands and has no supporting alpha helix as in the N lobe [2].	Domain
A, B, C, D	PF01298	C-lobe and N-lobe beta barrels of Tf-binding protein B (TbpB_B_D)	C-lobe and N-lobe beta barrels of Tf-binding protein B	Bacterial lipoproteins represent a large group of specialized membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis ...	Bacterial lipoproteins represent a large group of specialized membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence [1]. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialized uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf). TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a "handle" domain made up of four (N lobe) or eight (C lobe) beta strands [2]. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf [3]. This domain family is found in C and N lobe eight stranded beta barrel region of TbpB proteins. The eight-stranded barrel domains in N and C lobe draw comparisons to eight-stranded beta barrel outer-membrane protein W (OmpW). However, the barrel domains of TbpB have the hydrophobic residues line the inner surface of the beta barrels to create a stable hydrophobic core [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	TbpB	-	-	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR011250	Outer membrane protein/outer membrane enzyme PagP, beta-barrel	Homologous Superfamily
A, B, C, D	IPR001677	Transferrin-binding protein B, C-lobe/N-lobe beta-barrel domain	Domain
A, B, C, D	IPR038669	TbpB, N-lobe handle domain superfamily	Homologous Superfamily
A, B, C, D	IPR038197	TbpB, C-lobe handle domain superfamily	Homologous Superfamily
A, B, C, D	IPR035316	Transferrin-binding protein B, C-lobe handle domain	Domain

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.