2EKY | pdb_00002eky

Crystal Structure of hypothetical protein MJ1052 from Methanocaldococcus jannaschii (Form 1)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family 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)
H	d2ekyh_	Alpha and beta proteins (a+b)	Ferredoxin-like	MTH1187/YkoF-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
G	d2ekyg_	Alpha and beta proteins (a+b)	Ferredoxin-like	MTH1187/YkoF-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
F	d2ekyf_	Alpha and beta proteins (a+b)	Ferredoxin-like	MTH1187/YkoF-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
E	d2ekye_	Alpha and beta proteins (a+b)	Ferredoxin-like	MTH1187/YkoF-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
D	d2ekyd_	Alpha and beta proteins (a+b)	Ferredoxin-like	MTH1187/YkoF-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
C	d2ekyc_	Alpha and beta proteins (a+b)	Ferredoxin-like	MTH1187/YkoF-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
B	d2ekyb_	Alpha and beta proteins (a+b)	Ferredoxin-like	MTH1187/YkoF-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
A	d2ekya_	Alpha and beta proteins (a+b)	Ferredoxin-like	MTH1187/YkoF-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	MTH1187/YkoF-like	8058856	3000874	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	MTH1187/YkoF-like	8058856	3000874	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	MTH1187/YkoF-like	8058856	3000874	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	MTH1187/YkoF-like	8058856	3000874	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MTH1187/YkoF-like	8058856	3000874	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MTH1187/YkoF-like	8058856	3000874	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MTH1187/YkoF-like	8058856	3000874	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MTH1187/YkoF-like	8058856	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)
H	Thiamine_BP	e2ekyH1	A: a+b two layers	X: Alpha-beta plaits	H: MTH1187/YkoF-like (From Topology)	T: MTH1187/YkoF-like	F: Thiamine_BP	ECOD (1.6)
G	Thiamine_BP	e2ekyG1	A: a+b two layers	X: Alpha-beta plaits	H: MTH1187/YkoF-like (From Topology)	T: MTH1187/YkoF-like	F: Thiamine_BP	ECOD (1.6)
F	Thiamine_BP	e2ekyF1	A: a+b two layers	X: Alpha-beta plaits	H: MTH1187/YkoF-like (From Topology)	T: MTH1187/YkoF-like	F: Thiamine_BP	ECOD (1.6)
E	Thiamine_BP	e2ekyE1	A: a+b two layers	X: Alpha-beta plaits	H: MTH1187/YkoF-like (From Topology)	T: MTH1187/YkoF-like	F: Thiamine_BP	ECOD (1.6)
D	Thiamine_BP	e2ekyD1	A: a+b two layers	X: Alpha-beta plaits	H: MTH1187/YkoF-like (From Topology)	T: MTH1187/YkoF-like	F: Thiamine_BP	ECOD (1.6)
C	Thiamine_BP	e2ekyC1	A: a+b two layers	X: Alpha-beta plaits	H: MTH1187/YkoF-like (From Topology)	T: MTH1187/YkoF-like	F: Thiamine_BP	ECOD (1.6)
B	Thiamine_BP	e2ekyB1	A: a+b two layers	X: Alpha-beta plaits	H: MTH1187/YkoF-like (From Topology)	T: MTH1187/YkoF-like	F: Thiamine_BP	ECOD (1.6)
A	Thiamine_BP	e2ekyA1	A: a+b two layers	X: Alpha-beta plaits	H: MTH1187/YkoF-like (From Topology)	T: MTH1187/YkoF-like	F: Thiamine_BP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

InterPro: Protein Family Classification InterPro Database Homepage

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