P24931 (RUBY_DESVH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Rubrerythrin
Short name=Rr

Gene names

Name:	rbr
Ordered Locus Names:	DVU_3094

Organism

Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)

Taxonomic identifier

882 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

Protein attributes

Sequence length	191 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide By similarity.
Cofactor	Binds 3 Fe3+ ions per subunit.
Subunit structure	Homodimer. Possesses two rubredoxin-like centers and two non-sulfur oxo-bridged di-iron centers per dimer.
Subcellular location	Cytoplasm Potential.
Sequence similarities	Contains 1 ferritin-like diiron domain. Contains 1 rubredoxin-like domain.
Caution	Was originally thought to have inorganic pyrophosphatase activity.

Ontologies

Keywords
Biological process	Electron transport Transport
Cellular component	Cytoplasm
Ligand	Iron Metal-binding Zinc
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 transport Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	electron carrier activity Inferred from electronic annotation. Source: InterPro iron ion binding Inferred from direct assay Ref.8. Source: UniProtKB oxidoreductase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 191

191

Rubrerythrin

PRO_0000135064

Regions

Domain

1 – 146

146

Ferritin-like diiron

Domain

153 – 191

39

Rubredoxin-like

Sites

Metal binding

20

1

Zinc or iron 1

Metal binding

53

1

Iron 2

Metal binding

53

1

Zinc or iron 1

Metal binding

94

1

Iron 2

Metal binding

97

1

Zinc or iron 1

Metal binding

128

1

Iron 2

Metal binding

128

1

Zinc or iron 1

Metal binding

131

1

Iron 2

Metal binding

158

1

Iron 3

Metal binding

161

1

Iron 3

Metal binding

174

1

Iron 3

Metal binding

177

1

Iron 3

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

191

Helix Strand Turn

Details...

Helix

8 – 37

30

Helix

40 – 61

22

Helix

83 – 99

17

Helix

101 – 110

10

Turn

111 – 113

3

Helix

115 – 143

29

Beta strand

147 – 158

12

Turn

159 – 161

3

Beta strand

164 – 169

6

Turn

175 – 177

3

Helix

181 – 183

3

Beta strand

184 – 186

3

Sequences

	Sequence		Length	Mass (Da)
	P24931 [UniParc]. Last modified March 1, 1992. Version 1. Checksum: BCF8E9A2659F1138	FASTA	191	21,544
	10 20 30 40 50 60 MKSLKGSRTE KNILTAFAGE SQARNRYNYF GGQAKKDGFV QISDIFAETA DQEREHAKRL 70 80 90 100 110 120 FKFLEGGDLE IVAAFPAGII ADTHANLIAS AAGEHHEYTE MYPSFARIAR EEGYEEIARV 130 140 150 160 170 180 FASIAVAEEF HEKRFLDFAR NIKEGRVFLR EQATKWRCRN CGYVHEGTGA PELCPACAHP 190 KAHFELLGIN W

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and sequencing of the gene for rubrerythrin from Desulfovibrio vulgaris (Hildenborough)." Prickril B.C., Kurtz D.M. Jr., LeGall J., Voordouw G. Biochemistry 30:11118-11123(1991) [PubMed: 1932032] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	Lumppio H.L., Shenvi N.V., Garg R.P., Summers A.O., Kurtz D.M. Jr. Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"The primary structure of rubrerythrin, a protein with inorganic pyrophosphatase activity from Desulfovibrio vulgaris. Comparison with hemerythrin and rubredoxin." van Beeumen J.J., van Driessche G., Liu M.-Y., LeGall J. J. Biol. Chem. 266:20645-20653(1991) [PubMed: 1657933] [Abstract] Cited for: PROTEIN SEQUENCE.
[4]	"The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough." Heidelberg J.F., Seshadri R., Haveman S.A., Hemme C.L., Paulsen I.T., Kolonay J.F., Eisen J.A., Ward N.L., Methe B.A., Brinkac L.M., Daugherty S.C., DeBoy R.T., Dodson R.J., Durkin A.S., Madupu R., Nelson W.C., Sullivan S.A., Fouts D.E. , Haft D.H., Selengut J., Peterson J.D., Davidsen T.M., Zafar N., Zhou L., Radune D., Dimitrov G., Hance M., Tran K., Khouri H.M., Gill J., Utterback T.R., Feldblyum T.V., Wall J.D., Voordouw G., Fraser C.M. Nat. Biotechnol. 22:554-559(2004) [PubMed: 15077118] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Hildenborough / ATCC 29579 / NCIMB 8303.
[5]	"Nigerythrin and rubrerythrin from Desulfovibrio vulgaris each contain two mononuclear iron centers and two dinuclear iron clusters." Pierik A.J., Wolbert R.B.G., Portier G.L., Verhagen M.F.J.M., Hagen W.R. Eur. J. Biochem. 212:237-245(1993) [PubMed: 8383040] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-15, CHARACTERIZATION OF IRON-BINDING SITES.
[6]	"Intrapeptide sequence homology in rubrerythrin from Desulfovibrio vulgaris: identification of potential ligands to the diiron site." Kurtz D.M. Jr., Prickril B.C. Biochem. Biophys. Res. Commun. 181:337-341(1991) [PubMed: 1958203] [Abstract] Cited for: POSSIBLE BINUCLEAR IRON-SITES.
[7]	"Isolation and characterization of rubrerythrin, a non-heme iron protein from Desulfovibrio vulgaris that contains rubredoxin centers and a hemerythrin-like binuclear iron cluster." LeGall J., Prickril B.C., Moura I., Xavier A.V., Moura J.J.G., Huynh B.H. Biochemistry 27:1636-1642(1988) [PubMed: 2835096] [Abstract] Cited for: CHARACTERIZATION.
[8]	"The structure of Desulfovibrio vulgaris rubrerythrin reveals a unique combination of rubredoxin-like FeS4 and ferritin-like diiron domains." deMare F., Kurtz D.M. Jr., Nordlund P. Nat. Struct. Biol. 3:539-546(1996) [PubMed: 8646540] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
[9]	"Alternative metal-binding sites in rubrerythrin." Sieker L.C., Holmes M., Le Trong I., Turley S., Santarsiero B.D., Liu M.-Y., LeGall J., Stenkamp R.E. Nat. Struct. Biol. 6:308-309(1999) [PubMed: 10201393] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[10]	"The 1.9 A crystal structure of the 'as isolated' rubrerythrin from Desulfovibrio vulgaris: some surprising results." Sieker L.C., Holmes M., Le Trong I., Turley S., Liu M.-Y., LeGall J., Stenkamp R.E. J. Biol. Inorg. Chem. 5:505-513(2000) [PubMed: 10968622] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
[11]	"X-ray crystal structures of reduced rubrerythrin and its azide adduct: a structure-based mechanism for a non-heme diiron peroxidase." Jin S., Kurtz D.M. Jr., Liu Z.-J., Rose J., Wang B.-C. J. Am. Chem. Soc. 124:9845-9855(2002) [PubMed: 12175244] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.63 ANGSTROMS).
[12]	"Crystal structure studies on rubrerythrin: enzymatic activity in relation to the zinc movement." Li M., Liu M.-Y., LeGall J., Gui L.-L., Liao J., Jiang T., Zhang J.-P., Liang D.-C., Chang W.-R. J. Biol. Inorg. Chem. 8:149-155(2003) [PubMed: 12459910] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U82323 Genomic DNA. Translation: AAB39991.1.
AE017285 Genomic DNA. Translation: AAS97565.1.

PIR

A39492. A41191.

RefSeq

YP_012305.1. NC_002937.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1B71	X-ray	1.90	A	1-191	[»]
1DVB	X-ray	1.90	A	1-191	[»]
1JYB	X-ray	2.20	A	1-191	[»]
1LKM	X-ray	1.69	A	1-191	[»]
1LKO	X-ray	1.63	A	1-191	[»]
1LKP	X-ray	1.64	A	1-191	[»]
1QYB	X-ray	1.75	A	1-191	[»]
1RYT	X-ray	2.10	A	2-191	[»]
1S2Z	X-ray	1.75	A	1-191	[»]
1S30	X-ray	2.05	A	1-191	[»]

ProteinModelPortal

P24931.

SMR

P24931. Positions 1-191.

ModBase

Search...

Protein-protein interaction databases

STRING

P24931.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

2795966.

GenomeReviews

Gene locus DVU_3094 in contig AE017285_GR.

KEGG

dvu:DVU3094.

PATRIC

32065734. VBIDesVul119526_2807.

TIGR

DVU_3094.

Phylogenomic databases

eggNOG

COG1592.

HOGENOM

HBG700480.

OMA

NCGYLHE.

ProtClustDB

CLSK926802.

Enzyme and pathway databases

BioCyc

DVUL882:DVU_3094-MONOMER.

Family and domain databases

InterPro

IPR009040. Ferritin-like.
IPR012347. Ferritin-rel.
IPR009078. Ferritin/RR-like.
IPR024934. Rubredoxin-like_dom.
IPR004039. Rubredoxin-type_fold.
IPR003251. Rubrerythrin.
[Graphical view]

Gene3D

G3DSA:1.20.1260.10. Ferritin_rel. 1 hit.
G3DSA:2.20.28.10. Rubredox. 1 hit.

Pfam

PF02915. Rubrerythrin. 1 hit.
[Graphical view]

SUPFAM

SSF47240. Ferritin/RR_like. 1 hit.

PROSITE

PS50905. FERRITIN_LIKE. 1 hit.
PS50903. RUBREDOXIN_LIKE. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RUBY_DESVH

Accession

Primary (citable) accession number: P24931

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 1, 1992
Last sequence update:	March 1, 1992
Last modified:	January 25, 2012
This is version 105 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program