P24297 (RUBR_PYRFU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Rubredoxin
Short name=Rd

Gene names

Name:	rub
Ordered Locus Names:	PF1282

Organism

Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) [Reference proteome] [HAMAP]

Taxonomic identifier

186497 [NCBI]

Taxonomic lineage

cellular organisms › Archaea › Euryarchaeota › Thermococci › Thermococcales › Thermococcaceae › Pyrococcus › Pyrococcus furiosus

Protein attributes

Sequence length	54 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule.
Cofactor	Binds 1 Fe3+ ion per subunit.
Sequence similarities	Belongs to the rubredoxin family. Contains 1 rubredoxin-like domain.
Biophysicochemical properties	Temperature dependence: Extremely thermostable, being unaffected after incubation for 24 hours at 95 degrees Celsius.

Ontologies

Keywords
Biological process	Electron transport Transport
Ligand	Iron Metal-binding
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	electron transport chain Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	electron carrier activity Inferred from electronic annotation. Source: InterPro iron ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.3

Chain

2 – 54

53

Rubredoxin

PRO_0000135063

Regions

Domain

2 – 52

51

Rubredoxin-like

Sites

Metal binding

6

1

Iron

Metal binding

9

1

Iron

Metal binding

39

1

Iron

Metal binding

42

1

Iron

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

54

Helix Strand Turn

Details...

Beta strand

3 – 6

4

Turn

7 – 9

3

Beta strand

12 – 14

3

Turn

15 – 17

3

Helix

20 – 22

3

Helix

30 – 32

3

Turn

40 – 42

3

Helix

46 – 48

3

Beta strand

49 – 52

4

Sequences

	Sequence		Length	Mass (Da)
	P24297 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: 7181BBB4A3E8B1A8	FASTA	54	6,027
	10 20 30 40 50 MAKWVCKICG YIYDEDAGDP DNGISPGTKF EELPDDWVCP ICGAPKSEFE KLED

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Anaerobic microbes: oxygen detoxification without superoxide dismutase." Jenney F.E. Jr., Verhagen M.F.J.M., Cui X., Adams M.W.W. Science 286:306-309(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[2]	"Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences." Maeder D.L., Weiss R.B., Dunn D.M., Cherry J.L., Gonzalez J.M., DiRuggiero J., Robb F.T. Genetics 152:1299-1305(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[3]	"Determinants of protein hyperthermostability: purification and amino acid sequence of rubredoxin from the hyperthermophilic archaebacterium Pyrococcus furiosus and secondary structure of the zinc adduct by NMR." Blake P.R., Park J.-B., Bryant F.O., Aono S., Magnuson J.K., Eccleston E., Howard J.B., Summers M.F., Adams M.W.W. Biochemistry 30:10885-10895(1991) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-54. Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1.
[4]	"X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus." Day M.W., Hsu B.T., Joshua-Tor L., Park J.-B., Zhou Z.H., Adams M.W.W., Rees D.C. Protein Sci. 1:1494-1507(1992) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
[5]	"Solution-state structure by NMR of zinc-substituted rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus." Blake P.R., Park J.-B., Zhou Z.H., Hare D.R., Adams M.W.W., Summers M.F. Protein Sci. 1:1508-1521(1992) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR.
[6]	"Comparison of the X-ray structure of native rubredoxin from Pyrococcus furiosus with the NMR structure of the zinc-substituted protein." Blake P.R., Day M.W., Hsu B.T., Joshua-Tor L., Park J.-B., Hare D.R., Adams M.W.W., Rees D.C., Summers M.F. Protein Sci. 1:1522-1525(1992) [PubMed] [Europe PMC] [Abstract] Cited for: COMPARISON OF NMR STRUCTURE WITH X-RAY STRUCTURE.
[7]	"Crystal structure of rubredoxin from Pyrococcus furiosus at 0.95-A resolution, and the structures of N-terminal methionine and formylmethionine variants of Pf Rd. Contributions of N-terminal interactions to thermostability." Bau R., Rees D.C., Kurtz D.M. Jr., Scott R.A., Huang H., Adams M.W.W., Eidsness M.K. J. Biol. Inorg. Chem. 3:484-493(1998) Cited for: X-RAY CRYSTALLOGRAPHY (1.1 ANGSTROMS).
[8]	"Contribution of surface salt bridges to protein stability." Strop P., Mayo S.L. Biochemistry 39:1251-1255(2000) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF156097 Genomic DNA. Translation: AAF03228.1.
AE009950 Genomic DNA. Translation: AAL81406.1.

PIR

RUPF. T44570.

RefSeq

NP_579011.1. NC_003413.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BQ8	X-ray	1.10	A	1-54	[»]
1BQ9	X-ray	1.20	A	1-54	[»]
1BRF	X-ray	0.95	A	2-54	[»]
1CAA	X-ray	1.80	A	2-54	[»]
1CAD	X-ray	1.80	A	2-54	[»]
1IU5	X-ray	1.50	A	2-53	[»]
1IU6	neutron diffraction	1.60	A	2-53	[»]
1QCV	NMR	-	A	2-54	[»]
1RWD	NMR	-	A	2-53	[»]
1VCX	neutron diffraction	1.50	A	2-53	[»]
1ZRP	NMR	-	A	2-54	[»]
2PVX	X-ray	1.04	A/B/C/D/E/F/G/H	3-54	[»]
3KYU	X-ray	1.10	A	1-54	[»]
3KYV	X-ray	1.10	A	1-54	[»]
3KYW	X-ray	1.10	A	1-54	[»]
3KYX	Other	1.68	A	1-54	[»]
3KYY	X-ray	1.10	A	1-54	[»]
3RYG	neutron diffraction	1.75	A	1-54	[»]
3RZ6	neutron diffraction	1.75	A	1-54	[»]
3RZT	neutron diffraction	1.75	A	1-54	[»]
3SS2	neutron diffraction	1.75	A	1-54	[»]
4AR3	neutron diffraction	1.05	A	1-54	[»]
4AR4	neutron diffraction	1.38	A	1-54	[»]
4AR5	X-ray	1.00	A	1-54	[»]
4AR6	X-ray	0.92	A	1-54	[»]

ProteinModelPortal

P24297.

SMR

P24297. Positions 1-54.

ModBase

Search...

Protein-protein interaction databases

STRING

186497.PF1282.

Proteomic databases

PRIDE

P24297.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAL81406; AAL81406; PF1282.

GeneID

1469155.

KEGG

pfu:PF1282.

Phylogenomic databases

eggNOG

COG1773.

HOGENOM

HOG000223371.

OMA

FEMIAIG.

ProtClustDB

CLSK253564.

Family and domain databases

Gene3D

2.20.28.10. 1 hit.

InterPro

IPR024922. Rubredoxin.
IPR024934. Rubredoxin-like_dom.
IPR004039. Rubredoxin-type_fold.
IPR024935. Rubredoxin_dom.
IPR018527. Rubredoxin_Fe_BS.
[Graphical view]

Pfam

PF00301. Rubredoxin. 1 hit.
[Graphical view]

PIRSF

PIRSF000071. Rubredoxin. 1 hit.

PRINTS

PR00163. RUBREDOXIN.

PROSITE

PS00202. RUBREDOXIN. 1 hit.
PS50903. RUBREDOXIN_LIKE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P24297.

Entry information

Entry name

RUBR_PYRFU

Accession

Primary (citable) accession number: P24297
Secondary accession number(s): Q9UWP6

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 1, 1992
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 104 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program