2YVX | pdb_00002yvx

Crystal structure of magnesium transporter MgtE

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
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d2yvxd1	All alpha proteins	alpha-alpha superhelix	MgtE N-terminal domain-like	MgtE N-terminal domain-like	Magnesium transporter MgtE	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
D	d2yvxd2	Alpha and beta proteins (a+b)	CBS-domain pair	CBS-domain pair	CBS-domain pair	Magnesium transporter MgtE	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
D	d2yvxd3	Membrane and cell surface proteins and peptides	MgtE membrane domain-like	MgtE membrane domain-like	MgtE membrane domain-like	Mg2+ transporter MgtE	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
C	d2yvxc1	All alpha proteins	alpha-alpha superhelix	MgtE N-terminal domain-like	MgtE N-terminal domain-like	Magnesium transporter MgtE	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
C	d2yvxc2	Alpha and beta proteins (a+b)	CBS-domain pair	CBS-domain pair	CBS-domain pair	Magnesium transporter MgtE	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
C	d2yvxc3	Membrane and cell surface proteins and peptides	MgtE membrane domain-like	MgtE membrane domain-like	MgtE membrane domain-like	Mg2+ transporter MgtE	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d2yvxb1	All alpha proteins	alpha-alpha superhelix	MgtE N-terminal domain-like	MgtE N-terminal domain-like	Magnesium transporter MgtE	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d2yvxb2	Alpha and beta proteins (a+b)	CBS-domain pair	CBS-domain pair	CBS-domain pair	Magnesium transporter MgtE	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d2yvxb3	Membrane and cell surface proteins and peptides	MgtE membrane domain-like	MgtE membrane domain-like	MgtE membrane domain-like	Mg2+ transporter MgtE	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
A	d2yvxa1	All alpha proteins	alpha-alpha superhelix	MgtE N-terminal domain-like	MgtE N-terminal domain-like	Magnesium transporter MgtE	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
A	d2yvxa2	Alpha and beta proteins (a+b)	CBS-domain pair	CBS-domain pair	CBS-domain pair	Magnesium transporter MgtE	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
A	d2yvxa3	Membrane and cell surface proteins and peptides	MgtE membrane domain-like	MgtE membrane domain-like	MgtE membrane domain-like	Mg2+ transporter MgtE	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2 Family	MgtE membrane domain-like	8003832	4000203	SCOP2 (2022-06-29)
D	SCOP2 Family	MgtE N-terminal domain-like	8003835	4000290	SCOP2 (2022-06-29)
D	SCOP2 Family	CBS-domain pair	8003838	4000247	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	MgtE membrane domain-like	8003833	3000124	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	MgtE/FliG domain-like	8003836	3000127	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	CBS-domain pair	8003839	3000123	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	MgtE/FliG domain-like	8003836	3000127	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MgtE membrane domain-like	8003833	3000124	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CBS-domain pair	8003839	3000123	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CBS-domain pair	8003839	3000123	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MgtE/FliG domain-like	8003836	3000127	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MgtE membrane domain-like	8003833	3000124	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MgtE membrane domain-like	8003833	3000124	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MgtE/FliG domain-like	8003836	3000127	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CBS-domain pair	8003839	3000123	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)
D	MgtE	e2yvxD1	A: alpha duplicates or obligate multimers	X: Magnesium transporter MgtE membrane domain (From Topology)	H: Magnesium transporter MgtE membrane domain (From Topology)	T: Magnesium transporter MgtE membrane domain	F: MgtE	ECOD (1.6)
D	MgtE_N	e2yvxD2	A: alpha superhelices	X: Repetitive alpha hairpins	H: MgtE N-terminal domain-like (From Topology)	T: MgtE N-terminal domain-like	F: MgtE_N	ECOD (1.6)
D	IMPDH_2nd_1	e2yvxD3	A: a+b duplicates or obligate multimers	X: CBS-domain (From Topology)	H: CBS-domain (From Topology)	T: CBS-domain	F: IMPDH_2nd_1	ECOD (1.6)
C	MgtE	e2yvxC1	A: alpha duplicates or obligate multimers	X: Magnesium transporter MgtE membrane domain (From Topology)	H: Magnesium transporter MgtE membrane domain (From Topology)	T: Magnesium transporter MgtE membrane domain	F: MgtE	ECOD (1.6)
C	MgtE_N	e2yvxC2	A: alpha superhelices	X: Repetitive alpha hairpins	H: MgtE N-terminal domain-like (From Topology)	T: MgtE N-terminal domain-like	F: MgtE_N	ECOD (1.6)
C	IMPDH_2nd_1	e2yvxC3	A: a+b duplicates or obligate multimers	X: CBS-domain (From Topology)	H: CBS-domain (From Topology)	T: CBS-domain	F: IMPDH_2nd_1	ECOD (1.6)
B	MgtE	e2yvxB1	A: alpha duplicates or obligate multimers	X: Magnesium transporter MgtE membrane domain (From Topology)	H: Magnesium transporter MgtE membrane domain (From Topology)	T: Magnesium transporter MgtE membrane domain	F: MgtE	ECOD (1.6)
B	MgtE_N	e2yvxB2	A: alpha superhelices	X: Repetitive alpha hairpins	H: MgtE N-terminal domain-like (From Topology)	T: MgtE N-terminal domain-like	F: MgtE_N	ECOD (1.6)
B	IMPDH_2nd_1	e2yvxB3	A: a+b duplicates or obligate multimers	X: CBS-domain (From Topology)	H: CBS-domain (From Topology)	T: CBS-domain	F: IMPDH_2nd_1	ECOD (1.6)
A	MgtE	e2yvxA1	A: alpha duplicates or obligate multimers	X: Magnesium transporter MgtE membrane domain (From Topology)	H: Magnesium transporter MgtE membrane domain (From Topology)	T: Magnesium transporter MgtE membrane domain	F: MgtE	ECOD (1.6)
A	MgtE_N	e2yvxA2	A: alpha superhelices	X: Repetitive alpha hairpins	H: MgtE N-terminal domain-like (From Topology)	T: MgtE N-terminal domain-like	F: MgtE_N	ECOD (1.6)
A	IMPDH_2nd_1	e2yvxA3	A: a+b duplicates or obligate multimers	X: CBS-domain (From Topology)	H: CBS-domain (From Topology)	T: CBS-domain	F: IMPDH_2nd_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.25.60.10	Mainly Alpha	Alpha Horseshoe	MgtE N-terminal fold	MgtE N-terminal domain-like	CATH (4.3.0)
D	3.10.580.10	Alpha Beta	Roll	CBS-domain	CBS-domain	CATH (4.3.0)
D	1.10.357.20	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
C	1.25.60.10	Mainly Alpha	Alpha Horseshoe	MgtE N-terminal fold	MgtE N-terminal domain-like	CATH (4.3.0)
C	3.10.580.10	Alpha Beta	Roll	CBS-domain	CBS-domain	CATH (4.3.0)
C	1.10.357.20	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
B	1.25.60.10	Mainly Alpha	Alpha Horseshoe	MgtE N-terminal fold	MgtE N-terminal domain-like	CATH (4.3.0)
B	3.10.580.10	Alpha Beta	Roll	CBS-domain	CBS-domain	CATH (4.3.0)
B	1.10.357.20	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)
A	1.25.60.10	Mainly Alpha	Alpha Horseshoe	MgtE N-terminal fold	MgtE N-terminal domain-like	CATH (4.3.0)
A	3.10.580.10	Alpha Beta	Roll	CBS-domain	CBS-domain	CATH (4.3.0)
A	1.10.357.20	Mainly Alpha	Orthogonal Bundle	Tetracycline Repressor	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01769	Divalent cation transporter (MgtE)	Divalent cation transporter	-	Family
A, B, C, D	PF00571	CBS domain (CBS)	CBS domain	CBS domains are small intracellular modules that pair together to form a stable globular domain [2]. This family represents a single CBS domain. Pairs of these domains have been termed a Bateman domain [6]. CBS domains have been shown to bind ligands ...	CBS domains are small intracellular modules that pair together to form a stable globular domain [2]. This family represents a single CBS domain. Pairs of these domains have been termed a Bateman domain [6]. CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet [5]. CBS domains are found attached to a wide range of other protein domains suggesting that CBS domains may play a regulatory role making proteins sensitive to adenosyl carrying ligands. The region containing the CBS domains in Cystathionine-beta synthase is involved in regulation by S-AdoMet [4]. CBS domain pairs from AMPK bind AMP or ATP [5]. The CBS domains from IMPDH and the chloride channel CLC2 bind ATP [5].	Domain
A, B, C, D	PF03448	MgtE intracellular N domain (MgtE_N)	MgtE intracellular N domain	This domain is found at the N-terminus of eubacterial magnesium transporters of the MgtE family Pfam:PF01769. This domain is an intracellular domain that has an alpha-helical structure. The crystal structure of the MgtE transporter [1] shows two of 5 ...	This domain is found at the N-terminus of eubacterial magnesium transporters of the MgtE family Pfam:PF01769. This domain is an intracellular domain that has an alpha-helical structure. The crystal structure of the MgtE transporter [1] shows two of 5 magnesium ions are in the interface between the N domain and the CBS domains. In the absence of magnesium there is a large shift between the N and CBS domains.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Mg2+ transporter MgtE	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity monoatomic cation transmembrane transporter activity magnesium ion transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity monoatomic cation transmembrane transporter activity magnesium ion transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity	localization transport magnesium ion transport monoatomic ion transport monoatomic cation transport establishment of localization metal ion transport	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR046342	CBS domain superfamily	Homologous Superfamily
A, B, C, D	IPR006668	Magnesium transporter, MgtE intracellular domain	Domain
A, B, C, D	IPR038076	MgtE, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR000644	CBS domain	Domain
A, B, C, D	IPR036739	SLC41A/MgtE divalent cation transporters, integral membrane domain superfamily	Homologous Superfamily
A, B, C, D	IPR006667	SLC41A/MgtE, integral membrane domain	Domain
A, B, C, D	IPR006669	Magnesium transporter MgtE	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	OPM	Transmembrane	Alpha-helical polytopic	Magnesium ion transporter-E (MgtE)	Magnesium ion transporter-E (MgtE)

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Other Ion Channels	MgtE Mg²⁺ Transporter

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.