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PR00163

Identifier
RUBREDOXIN  [View Relations]  [View Alignment]  
Accession
PR00163
No. of Motifs
2
Creation Date
15-JAN-1994  (UPDATE 24-JUN-1999)
Title
Rubredoxin signature
Database References

PROSITE; PS00202 RUBREDOXIN
BLOCKS; BL00202
PFAM; PF00301 rubredoxin
INTERPRO; IPR001052
PDB; 7RXN
SCOP; 7RXN
CATH; 7RXN
Literature References
1. ADMAN, E.T., SIEKER, L.C. AND JENSEN, L.H.
Structure of rubredoxin from Desulfovibrio vulgaris at 1.5 Angstroms
resolution.
J.MOL.BIOL. 217(2) 337-352 (1991).
 
2. MEYER, J., GAGNON, J., SIEKER, L.C., VANDORSSELAER, A. AND MOULIS, J.M.
Rudredoxin from Clostridium thermosaccharolyticum - Amino acid sequence,
mass spectrometric and preliminary crystallographic data.
BIOCHEM.J. 271(3) 839-841 (1990).
 
3. BACHMAYER, H., YASUNOBU, K.T., PEEL, J.L. AND MAYHEW, S.
Non-heme iron proteins.
J.BIOL.CHEM. 243 1022-1030 (1968).
 
4. CHEN, J.C. AND MORTENSEN, L.E.
2 Open reading frames (ORFs) identified near the hydrogenase structural
genes in Azotobacter vinelandii, the 1st ORF may encode for a polypeptide
similar to rubredoxins.
BIOCHIM.BIOPHYS.ACTA 1131(1) 122-124 (1992).

Documentation
Rubredoxin is a low molecular weight non-haem iron-containing bacterial
protein involved in electron transfer [1,2], sometimes replacing ferredoxin
as an electron carrier [3]. Its active site contains an iron atom co-
ordinated by the sulphurs of 4 conserved Cys residues residing on 2 loops
[2,3], which are the most well-conserved regions of the protein [3]. In
some species, the rubredoxin gene is closely linked to the dehydrogenase
gene, and its transcription is required for dehydrogenase activity [4]. The
reason for this is as yet unknown, but rubredoxin may act as a source of
electrons for the molecular hydrogen-splitting activity of the
dehydrogenase [4].
 
RUBREDOXIN is a 2-element fingerprint that provides a signature for the 
rubredoxins. The fingerprint was derived from an initial alignment of 7
sequences: motifs 1 and 2 span the 2 loops involved in binding the
iron atom - motif 2 includes the region encoded by PROSITE pattern
RUBREDOXIN (PS00202), which contains 2 of the iron-binding Cys residues.
Two iterations on OWL22.1 were required to reach convergence, at which
point a true set comprising 23 sequences was identified.
 
An update on SPTR37_9f identified a true set of 38 sequences.
Summary Information
38 codes involving  2 elements
Composite Feature Index
23838
12
True Positives
HUPJ_RHOCA    O05893        O05894        O26258        
O26259 O28920 O29381 P73068
P94698 P95500 P96745 Q46496
Q46877 Q58145 Q58150 RUB1_PSEOL
RUB2_PSEOL RUBL_AZOVI RUBL_BRAJA RUBL_RHILV
RUBR_ACICA RUBR_ALCEU RUBR_AZOCH RUBR_BUTME
RUBR_CHLLT RUBR_CLOPA RUBR_CLOPE RUBR_CLOST
RUBR_CLOTS RUBR_DESDE RUBR_DESGI RUBR_DESVH
RUBR_DESVM RUBR_HELMO RUBR_MEGEL RUBR_PEPAS
RUBR_PYRFU RUBR_TREPA
Sequence Titles
HUPJ_RHOCA  PROBABLE RUBREDOXIN HUPJ - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA). 
O05893 RUBB - MYCOBACTERIUM TUBERCULOSIS.
O05894 RUBA - MYCOBACTERIUM TUBERCULOSIS.
O26258 RUBREDOXIN - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O26259 RUBREDOXIN - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O28920 RUBREDOXIN (RD-2) - ARCHAEOGLOBUS FULGIDUS.
O29381 RUBREDOXIN (RD-1) - ARCHAEOGLOBUS FULGIDUS.
P73068 RUBREDOXIN - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
P94698 RUBREDOXIN-LIKE PROTEIN - DESULFOVIBRIO VULGARIS.
P95500 RUBREDOXIN - PSEUDOMONAS HYDROGENOVORA.
P96745 RUBREDOXIN - CLOSTRIDIUM BUTYRICUM.
Q46496 RUBREDOXIN - DESULFOARCULUS BAARSII (DESULFOVIBRIO BAARSII).
Q46877 ORF_O479 - ESCHERICHIA COLI.
Q58145 RUBREDOXIN - METHANOCOCCUS JANNASCHII.
Q58150 RUBREDOXIN - METHANOCOCCUS JANNASCHII.
RUB1_PSEOL RUBREDOXIN 1 - PSEUDOMONAS OLEOVORANS.
RUB2_PSEOL RUBREDOXIN 2 - PSEUDOMONAS OLEOVORANS.
RUBL_AZOVI RUBREDOXIN IN UPTAKE HYDROGENASE OPERON - AZOTOBACTER VINELANDII.
RUBL_BRAJA PROBABLE RUBREDOXIN HUPI - BRADYRHIZOBIUM JAPONICUM.
RUBL_RHILV PROBABLE RUBREDOXIN HUPI - RHIZOBIUM LEGUMINOSARUM (BIOVAR VICIAE).
RUBR_ACICA RUBREDOXIN (RD) - ACINETOBACTER CALCOACETICUS.
RUBR_ALCEU RUBREDOXIN (RD) - ALCALIGENES EUTROPHUS.
RUBR_AZOCH RUBREDOXIN IN UPTAKE HYDROGENASE OPERON - AZOTOBACTER CHROOCOCCUM MCD 1.
RUBR_BUTME RUBREDOXIN (RD) - BUTYRIBACTERIUM METHYLOTROPHICUM.
RUBR_CHLLT RUBREDOXIN (RD) - CHLOROBIUM LIMICOLA F.SP. THIOSULFATOPHILUM.
RUBR_CLOPA RUBREDOXIN (RD) - CLOSTRIDIUM PASTEURIANUM.
RUBR_CLOPE RUBREDOXIN (RD) - CLOSTRIDIUM PERFRINGENS.
RUBR_CLOST RUBREDOXIN (RD) - CLOSTRIDIUM STICKLANDII.
RUBR_CLOTS RUBREDOXIN (RD) - CLOSTRIDIUM THERMOSACCHAROLYTICUM (THERMOANAEROBACTERIUM THERMOSACCHAROLYTICUM).
RUBR_DESDE RUBREDOXIN (RD) - DESULFOVIBRIO DESULFURICANS.
RUBR_DESGI RUBREDOXIN (RD) - DESULFOVIBRIO GIGAS.
RUBR_DESVH RUBREDOXIN (RD) - DESULFOVIBRIO VULGARIS (STRAIN HILDENBOROUGH).
RUBR_DESVM RUBREDOXIN (RD) - DESULFOVIBRIO VULGARIS (STRAIN MIYAZAKI).
RUBR_HELMO RUBREDOXIN - HELIOBACILLUS MOBILIS.
RUBR_MEGEL RUBREDOXIN (RD) - MEGASPHAERA ELSDENII.
RUBR_PEPAS RUBREDOXIN (RD) - PEPTOSTREPTOCOCCUS ASACCHAROLYTICUS (PEPTOCOCCUS ASACCHAROLYTICUS).
RUBR_PYRFU RUBREDOXIN (RD) - PYROCOCCUS FURIOSUS.
RUBR_TREPA RUBREDOXIN (RD) - TREPONEMA PALLIDUM.
Scan History
OWL22_1    2  100  NSINGLE    
OWL26_0 1 100 NSINGLE
SPTR37_9f 1 150 NSINGLE
Initial Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
KYTCTVCGYIYDPEDGD NRL_5RXN 3 3 -
KYVCNVCGYEYDPAEHD RUBR_DESDE 3 3 -
KYECSICGYIYDEAEGD RUBR_MEGEL 3 3 -
KYVCSVCGYVYDPADGE RUBR_CHLLT 3 3 -
RMECGICWHVYDPAEGD RUBL_RHILV 17 17 -
RLECKICWWEYDPEVGD RUBR_ALCEU 25 25 -
RYQCPDCQYIYDENKGE RUB1_PSEOL 3 3 -

Motif 2 width=17
Element Seqn Id St Int Rpt
IPKDWACPDCAVRDKVD RUB1_PSEOL 33 13 -
IPDDWVCPLCGVGKDEF NRL_5RXN 33 13 -
LPDDWCCPVCGVSKDQF RUBR_DESDE 26 6 -
LPADWVCPTCGADKDAF RUBR_MEGEL 32 12 -
LPEDWVCPVCGVDKDLF RUBR_CHLLT 33 13 -
LTEDWRCPNCDALQSKF RUBL_RHILV 47 13 -
LPAHWRCPNCDGEAEQF RUBR_ALCEU 55 13 -
Final Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
KYVCTVCGYEYDPAEGD RUBR_DESVH 3 3 -
KYVCTVCGYEYDPAEGD RUBR_DESVM 3 3 -
KYQCTICGYVYDEAEGD O29381 3 3 -
KYVCDICGYVYDPAVGD RUBR_BUTME 3 3 -
IYVCTVCGYEYDPAKGD RUBR_DESGI 3 3 -
KWVCKICGYIYDEDAGD RUBR_PYRFU 2 2 -
KWQCTVCGYIYDPEVGD RUBR_CLOTS 3 3 -
KYICTVCGYIYDEAAGD P96745 3 3 -
KYVCNVCGYEYDPAEHD RUBR_DESDE 3 3 -
KYECSICGYIYDEAEGD RUBR_MEGEL 3 3 -
KYVCTVCGYVYDPEVGD RUBR_CLOST 3 3 -
KYECQVCGYVYDEAEGD O28920 22 22 -
KFICDVCGYIYDPAVGD RUBR_CLOPE 3 3 -
KYVCSVCGYVYDPADGE RUBR_CHLLT 3 3 -
KYTCTVCGYIYNPEDGD RUBR_CLOPA 3 3 -
KYVCQMCGYIYDPEEGD O26259 3 3 -
KYGCLVCGYVYDPAKGD RUBR_HELMO 3 3 -
KYVCGVCVYEYDPAKGD Q46496 3 3 -
KYQCIVCGWIYDEAEGW RUBR_ACICA 3 3 -
IMECKICWTPYDPASGD HUPJ_RHOCA 25 25 -
KWICITCGHIYDEALGD RUB2_PSEOL 120 120 -
RLECGICWTVYDPADGD RUBL_BRAJA 18 18 -
KFECTLCGYIYDPALVG RUBR_PEPAS 3 3 -
RMECGICWHVYDPAEGD RUBL_RHILV 17 17 -
KLECKICWWVYDPAVGD P95500 25 25 -
VLECKICWQRYDPAEGD RUBL_AZOVI 21 21 -
RLECKICWWEYDPEVGD RUBR_ALCEU 25 25 -
VLECKICWHRYDPAVGD RUBR_AZOCH 21 21 -
RYKCRVCGYIYDPEKGE O26258 13 13 -
LFRCIQCGFEYDEALGW O05893 6 6 -
RYQCPDCQYIYDENKGE RUB1_PSEOL 3 3 -
TYMCDLCGWGYNPEVGD RUBR_TREPA 3 3 -
AYRCPVCDYVYDEANGD O05894 3 3 -
RMQCSVCQWIYDPAKGE Q46877 425 425 -
RCQTVNCGYVYDPDRGD P94698 9 9 -
KYKCKVCGWVYDPLKGD Q58145 21 21 -
NHECRACGYVYIPSQGD P73068 17 17 -
ARYQCMCGWVYDEDKGE Q58150 5 5 -

Motif 2 width=17
Element Seqn Id St Int Rpt
LPADWVCPVCGAPKSEF RUBR_DESVH 33 13 -
VPADWVCPICGAPKSEF RUBR_DESVM 33 13 -
LPDDWVCPVCGATKDQF O29381 33 13 -
LPEDWVCPECGVSKDEF RUBR_BUTME 33 13 -
LPDDWACPVCGASKDAF RUBR_DESGI 33 13 -
LPDDWVCPICGAPKSEF RUBR_PYRFU 32 13 -
LPDDWVCPDCGVGKDQF RUBR_CLOTS 33 13 -
IPDDWVCPLCGVPKSDF P96745 33 13 -
LPDDWCCPVCGVSKDQF RUBR_DESDE 26 6 -
LPADWVCPTCGADKDAF RUBR_MEGEL 32 12 -
IPEDWVCPLCGVGKDQF RUBR_CLOST 33 13 -
LPDDWVCPVCGASKDQF O28920 52 13 -
IPDDWVCPLCGVDKSQF RUBR_CLOPE 33 13 -
LPEDWVCPVCGVDKDLF RUBR_CHLLT 33 13 -
IPDDWVCPLCGVGKDQF RUBR_CLOPA 33 13 -
LPDDWVCPVCGVGKDQF O26259 33 13 -
LPADWVCPLCGVSKDEF RUBR_HELMO 33 13 -
LPADWSCPVCGASKDQF Q46496 33 13 -
IPDDWTCPDCGVSKVDF RUBR_ACICA 33 13 -
LPEDWHCPNCDAPKAQF HUPJ_RHOCA 55 13 -
IPDDWCCPDCGATKEDY RUB2_PSEOL 150 13 -
LPEEWHCPNCDAPKSKF RUBL_BRAJA 48 13 -
VSENWVCPLCGAGKEDF RUBR_PEPAS 32 12 -
LTEDWRCPNCDALQSKF RUBL_RHILV 47 13 -
LPPHWRCPNCDGDADQF P95500 55 13 -
LPAHWRCPRCDGDREQF RUBL_AZOVI 51 13 -
LPAHWRCPNCDGEAEQF RUBR_ALCEU 55 13 -
LPAHWRCPQCDGDREQF RUBR_AZOCH 51 13 -
LPETWRCPSCGAKKKMF O26258 43 13 -
IPDDWSCPDCGAAKSDF O05893 36 13 -
IPKDWACPDCAVRDKVD RUB1_PSEOL 33 13 -
LPDHWECPLCGVDKTSF RUBR_TREPA 33 13 -
IPDDWCCPDCAVREKVD O05894 33 13 -
VPDNFLCPECSLGKDVF Q46877 455 13 -
LPDEWRCPICKATKKCF P94698 39 13 -
LPDTWICPVCRGKVGKE Q58145 51 13 -
LPLNWKCPVCGAPRNYF P73068 47 13 -
LPDTFRCPQCGLGKNAF Q58150 35 13 -