Annotations: 1VK8

CRYSTAL STRUCTURE OF A PUTATIVE THIAMINE BIOSYNTHESIS/SALVAGE PROTEIN (TM0486) FROM THERMOTOGA MARITIMA AT 1.80 A RESOLUTION

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	d1vk8a_	Alpha and beta proteins (a+b)	Ferredoxin-like	MTH1187/YkoF-like	MTH1187-like	Hypothetical protein TM0486	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1vk8b_	Alpha and beta proteins (a+b)	Ferredoxin-like	MTH1187/YkoF-like	MTH1187-like	Hypothetical protein TM0486	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
C	d1vk8c_	Alpha and beta proteins (a+b)	Ferredoxin-like	MTH1187/YkoF-like	MTH1187-like	Hypothetical protein TM0486	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
D	d1vk8d_	Alpha and beta proteins (a+b)	Ferredoxin-like	MTH1187/YkoF-like	MTH1187-like	Hypothetical protein TM0486	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	MTH1187-like	8028987	4000648	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MTH1187/YkoF-like	8041366	3000874	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	MTH1187/YkoF-like	8041366	3000874	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MTH1187/YkoF-like	8041366	3000874	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MTH1187/YkoF-like	8041366	3000874	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	Thiamine_BP	e1vk8A1	A: a+b two layers	X: Alpha-beta plaits	H: MTH1187/YkoF-like	T: MTH1187/YkoF-like	F: Thiamine_BP	ECOD (v294.2)
B	RNase_P_Rpp14	e1vk8B1	A: beta barrels	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.2)
C	RNase_P_Rpp14	e1vk8C1	A: beta barrels	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.2)
D	RNase_P_Rpp14	e1vk8D1	A: beta barrels	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.930	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	3.30.70.930	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
C	3.30.70.930	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
D	3.30.70.930	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01910	Thiamine-binding protein (Thiamine_BP)	Thiamine-binding protein	The crystal structure of two of these members shows that this domain has a ferredoxin like fold and is likely to exists as at least homodimers. Sulphate ions are are located at the dimer interfaces, which are thought to confer additional stability. ...	The crystal structure of two of these members shows that this domain has a ferredoxin like fold and is likely to exists as at least homodimers. Sulphate ions are are located at the dimer interfaces, which are thought to confer additional stability. Although the function of this domain remains to be identified, its structure suggests a role in protein-protein interactions possibly regulated by the binding of small-molecule ligands [1]. Solution of the structure of the hyperthermophilic anaerobic Thermotoga maritima sequence, UniProtKB:Q9WYV6, shows that this has a beta-alpha-beta-beta-alpha-beta ferredoxin-like fold and assembles as a homotetramer. It was possible to identify a pocket in each monmer that bound an unidentified ligand. It was also found that it bound charged thiamine though not hydroxymethyl pyrimidine. It is proposed that it is transporting charged thiamine around the cytoplasm. Under oxidative conditions this bacterium is under stress, and the transcriiptional unit within which this protein is expressed is up-regulated in these conditions, suggesting that the chelation of cytoplasmic thaimine is part of the response mechanism to such oxidatvie stress, which is mediated by this family [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	hypothetical protein TM0486	cation binding vitamin binding thiamine binding binding ion binding alcohol binding heterocyclic compound binding small molecule binding sulfur compound binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029756	MTH1187/YkoF-like	Homologous Superfamily
A, B, C, D	IPR051614	UPF0045 domain-containing protein	Family
A, B, C, D	IPR002767	Thiamine-binding protein	Domain

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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.