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PR00352

Identifier
3FE4SFRDOXIN  [View Relations]  [View Alignment]  
Accession
PR00352
No. of Motifs
3
Creation Date
05-JUN-1995  (UPDATE 22-JUN-1999)
Title
3Fe-4S ferredoxin signature
Database References

INTERPRO; IPR001080
PDB; 1FXR; 2FXB
SCOP; 1FXR; 2FXB
CATH; 1FXD; 2FXB
Literature References
1. O'KEEFE, D.P., GIBSON, K.J., EMPTAGE, M.H., LENSTRA, R., ROMESSER, J.A.,
LITLE, P.J. AND OMER, C.A.
Ferredoxins from two sulfonylurea herbicide monooxygenase systems in 
Streptomyces griseolus. 
BIOCHEMISTRY 30 447-455 (1991).
 
2. TROWER, M.K., LENSTRA, R., OMER, C., BUCHHOLZ, S.E. AND SARIASLANI, F.S.
Cloning, nucleotide sequence determination and expression of the genes 
encoding cytochrome P-450soy (soyC) and ferredoxinsoy (soyB) from 
Streptomyces griseus
MOL.MICROBIOL. 6 2125-2134 (1992); ERRATUM: MOL.MICROBIOL. 7 1024-1025 (1993).
 
3. TULLY, R.E. AND KEISTER, D.L.
Cloning and mutagenesis of a cytochrome P-450 locus from  Bradyrhizobium 
japonicum that is expressed anaerobically and symbiotically.
APPL.ENVIRON.MICROBIOL. 59 4136-4142 (1993).
 
4. CRESPI, M., VEREECKE, D.M., TEMMERMAN, W.G., VAN MONTAGU, M. AND 
DESOMER, J.
The fas operon of Rhodococcus fascians encodes new genes required for
efficient fasciation of host plants.
J.BACTERIOL. 176 2492-2501 (1994).
 
5. BUSSE, S.C., LA MAR, G.N., YU, L.P., HOWARD, J.B., SMITH, E.T., 
ZHOU, Z.H. AND ADAMS, M.W.
Proton NMR investigation of the oxidized three-iron clusters in the 
ferredoxins from the hyperthermophilic archae Pyrococcus furiosus and
Thermococcus litoralis.
BIOCHEMISTRY 31 11952-11962 (1992).

Documentation
In a few bacterial P450-containing systems, the transfer of electrons from
flavoprotein reductase to P450 is mediated by 3Fe-4S ferredoxins [1-4].
Despite functional similarity of such ferredoxins to the adrenodoxin
family, they do not share sequence similarity. On the other hand, 3Fe-4S 
proteins seem to be similar to some mono-[4Fe-4S] cluster ferredoxins, 
but lack a fourth cysteine residue conserved in 4Fe-4S sequences [1]. It
has been shown experimentally that the 4Fe-4S cluster of related
ferredoxins from archaebacteria easily converts to a 3Fe-4S cluster [5].
 
3D structures are now known for a number of ferredoxins. The fold belongs
to the alpha + beta class, with 3 helices and 4 strands forming a barrel-
like structure, and an extruded loop containing 3 of the 4 cysteinyl
residues of the iron-sulphur cluster.                    
 
3FE4SFRDOXIN is a 3-element fingerprint that provides a signature for 
3Fe-4S ferredoxins. The fingerprint was derived from an initial alignment 
of 8 sequences: the motifs each contain invariant Cys residues contributing
to the cluster - motifs 1 and 2 are adjacent, spanning the second invariant
Cys (in 4Fe-4S ferredoxins that are similar to 3Fe-4S proteins, motif 1
contains an extra Cys residue contributing to the 4Fe-4S cluster). Three
iterations on OWL26.0 were required to reach convergence, at which point a
true set comprising 15 sequences was identified. Nine partial matches were
also found: these include bacterial 4Fe-4S ferredoxins and a hypothetical
protein involved in the biosynthesis of candicidin (PABT_STRGR).
 
An update on SPTR37_9f identified a true set of 26 sequences, and 12
partial matches.
Summary Information
  26 codes involving  3 elements
12 codes involving 2 elements
Composite Feature Index
3262626
210212
123
True Positives
FE45_BRAJA    FE45_RHISN    FER1_DESAF    FER1_DESDN    
FER1_STRGO FER2_DESVM FER2_STRGO FERS_STRGR
FER_BACST FER_BACSU FER_BACTH FER_MOOTH
FER_PYRFU FER_THELI FER_THEMA O27205
O27847 O30071 O85696 O87593
P71820 Q49180 Q50784 Q55980
Q56300 YSAA_ECOLI
True Positive Partials
Codes involving 2 elements
FAS2_RHOFA FER_DESGI FER_SULAC FER_SULS7
O26499 O27597 O32423 O74028
P81293 Q54301 Q58566 Q59575
Sequence Titles
FE45_BRAJA  PUTATIVE P450-SYSTEM 3FE-3S FERREDOXIN - BRADYRHIZOBIUM JAPONICUM. 
FE45_RHISN PUTATIVE P450-SYSTEM 3FE-3S FERREDOXIN - RHIZOBIUM SP. (STRAIN NGR234).
FER1_DESAF FERREDOXIN I - DESULFOVIBRIO AFRICANUS.
FER1_DESDN FERREDOXIN I - DESULFOVIBRIO DESULFURICANS (STRAIN NORWAY 4).
FER1_STRGO FERREDOXIN 1 (FD-1) - STREPTOMYCES GRISEOLUS.
FER2_DESVM FERREDOXIN II (FD II) - DESULFOVIBRIO VULGARIS (STRAIN MIYAZAKI).
FER2_STRGO FERREDOXIN 2 (FD-2) - STREPTOMYCES GRISEOLUS.
FERS_STRGR FERREDOXIN SOY - STREPTOMYCES GRISEUS.
FER_BACST FERREDOXIN - BACILLUS STEAROTHERMOPHILUS.
FER_BACSU FERREDOXIN - BACILLUS SUBTILIS.
FER_BACTH FERREDOXIN - BACILLUS THERMOPROTEOLYTICUS.
FER_MOOTH FERREDOXIN - MOORELLA THERMOACETICA (CLOSTRIDIUM THERMOACETICUM).
FER_PYRFU FERREDOXIN - PYROCOCCUS FURIOSUS.
FER_THELI FERREDOXIN - THERMOCOCCUS LITORALIS.
FER_THEMA FERREDOXIN - THERMOTOGA MARITIMA.
O27205 POLYFERREDOXIN (MVHB) - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O27847 FERREDOXIN - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O30071 FERREDOXIN (FDX-2) - ARCHAEOGLOBUS FULGIDUS.
O85696 PUTATIVE FERREDOXIN - STREPTOMYCES LIVIDANS.
O87593 PUTATIVE FERREDOXIN - STREPTOMYCES COELICOLOR.
P71820 PROBABLE FERREDOXIN - MYCOBACTERIUM TUBERCULOSIS.
Q49180 POLYFERREDOXIN MVHB - METHANOTHERMUS FERVIDUS.
Q50784 FERREDOXIN - METHANOBACTERIUM THERMOAUTOTROPHICUM.
Q55980 HYPOTHETICAL 15.1 KD PROTEIN - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
Q56300 4FE-4S FERREDOXIN - THERMOCOCCUS SP. JDF-3.
YSAA_ECOLI PUTATIVE ELECTRON TRANSPORT PROTEIN YSAA - ESCHERICHIA COLI.

FAS2_RHOFA FERREDOXIN FAS2 - RHODOCOCCUS FASCIANS.
FER_DESGI FERREDOXIN II - DESULFOVIBRIO GIGAS.
FER_SULAC FERREDOXIN - SULFOLOBUS ACIDOCALDARIUS.
FER_SULS7 FERREDOXIN - SULFOLOBUS SP. (STRAIN 7).
O26499 POLYFERREDOXIN - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O27597 TUNGSTEN FORMYLMETHANOFURAN DEHYDROGENASE, SUBUNIT F - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O32423 FERREDOXIN - SULFOLOBUS SOLFATARICUS.
O74028 TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE ISOENZYME II SUBUNIT F (EC 1.2.99.5) (POLYFERREDOXIN) - METHANOBACTERIUM WOLFEI.
P81293 POLYFERREDOXIN - METHANOCOCCUS JANNASCHII.
Q54301 FERREDOXIN - STREPTOMYCES HYGROSCOPICUS.
Q58566 TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE ISOENZYME II SUBUNIT F (EC 1.2.99.5) (POLYFERREDOXIN) - METHANOCOCCUS JANNASCHII.
Q59575 TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE ISOENZYME II SUBUNIT F (EC 1.2.99.5) (POLYFERREDOXIN) - METHANOBACTERIUM THERMOAUTOTROPHICUM (STRAIN MARBURG / DSM 2133).
Scan History
OWL26_0    3  100  NSINGLE    
SPTR37_9f 3 120 NSINGLE
Initial Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
VNERRCFGSGQC S42053 5 5 -
VDQDLCGTSGQC BJU126783 5 5 -
VDQDLCIACGTC FER_CLOTH 5 5 -
VDQDKCCGAGSC FER2_STRGO 5 5 -
VDQDECIACESC FER1_DESAF 6 6 -
VDKERCVGAGMC FERS_STRGR 5 5 -
ADRTVCVGAGLC FER1_STRGO 6 6 -
VDKETCIACGAC FER_BACST 6 6 -

Motif 2 width=11
Element Seqn Id St Int Rpt
CALTAPDVFTQ FERS_STRGR 16 -1 -
CALTAPGVFDQ FER1_STRGO 17 -1 -
CGAAAPDIYDY FER_BACST 17 -1 -
CVLVAPEVFEQ S42053 16 -1 -
CVLTLPGTFRQ BJU126783 16 -1 -
CIDLCPSVFDW FER_CLOTH 16 -1 -
CVLAAPDVFDQ FER2_STRGO 16 -1 -
CVEIAPGAFAM FER1_DESAF 17 -1 -

Motif 3 width=13
Element Seqn Id St Int Rpt
VRLAASQCPVAHS BJU126783 48 21 -
VREAATICPAAAI FER2_STRGO 48 21 -
VEEAMDTCPVQSI FER1_DESAF 47 19 -
VGEAVRACPVGAV FERS_STRGR 48 21 -
AREAGHLCPSGAV FER1_STRGO 49 21 -
MMDAFEGCPTESI FER_BACST 54 26 -
VRAAARSCPATAI S42053 47 20 -
ARESVNECPTEAI FER_CLOTH 48 21 -
Final Motifs
Motif 1  width=12
Element Seqn Id St Int Rpt
IDKDTCIGAGQC O85696 5 5 -
VDKDACIGCGVC FER_THELI 5 5 -
VDQDTCIGDAIC FER_PYRFU 6 6 -
VDQDKCCGAGSC FER2_STRGO 5 5 -
VDADACIGCGVC FER_THEMA 5 5 -
VDRDLCIGCGTC O30071 5 5 -
IDQDVCIGDAIC Q56300 7 7 -
IDHEECIGCESC FER1_DESDN 4 4 -
VDQDECIACESC FER1_DESAF 6 6 -
VDKERCVGAGMC FERS_STRGR 5 5 -
VDQDLCIACGTC FER_MOOTH 5 5 -
IDEDTCIKCGVC O27205 172 172 -
IDEDTCIKCGVC Q50784 172 172 -
IDQDLCGTTGQC FE45_RHISN 5 5 -
LDQDECMACESC FER2_DESVM 6 6 -
VDKDTCIACGAC FER_BACSU 6 6 -
ADRTVCVGAGLC FER1_STRGO 6 6 -
IDEEKCIKCGIC Q49180 172 172 -
VDKETCIACGAC FER_BACTH 6 6 -
VDEVTCIGCKNC Q55980 48 48 -
IDQDLCTGDGIC O87593 18 18 -
VDKETCIACGAC FER_BACST 6 6 -
VDQDLCGTSGQC FE45_BRAJA 5 5 -
ADATKCIGCRTC YSAA_ECOLI 7 7 -
LDRTMCISCGNC O27847 6 6 -
ADRDLCQGHAMC P71820 6 6 -

Motif 2 width=11
Element Seqn Id St Int Rpt
CALTAPGVFIQ O85696 16 -1 -
CASICPDVFEM FER_THELI 16 -1 -
CASLCPDVFEM FER_PYRFU 17 -1 -
CVLAAPDVFDQ FER2_STRGO 16 -1 -
CENLCPDVFQL FER_THEMA 16 -1 -
CEEICPEVFRL O30071 16 -1 -
CASLCPDVFEM Q56300 18 -1 -
CVELCPEVFAM FER1_DESDN 15 -1 -
CVEIAPGAFAM FER1_DESAF 17 -1 -
CALTAPDVFTQ FERS_STRGR 16 -1 -
CIDLCPSVFDW FER_MOOTH 16 -1 -
CVEACPGDFIV O27205 222 38 -
CVEACPGDFIV Q50784 222 38 -
CVLTLPGTFRQ FE45_RHISN 16 -1 -
CVELCPEAFRM FER2_DESVM 17 -1 -
CGAAAPDIYDY FER_BACSU 17 -1 -
CALTAPGVFDQ FER1_STRGO 17 -1 -
CVEICPGGFIE Q49180 222 38 -
CGAAAPDIYDY FER_BACTH 17 -1 -
CAHVAPNTFTI Q55980 59 -1 -
CAQYAPEVFEL O87593 29 -1 -
CGAAAPDIYDY FER_BACST 17 -1 -
CVLTLPGTFRQ FE45_BRAJA 16 -1 -
CAALSPDEFIS YSAA_ECOLI 32 13 -
CIDSCPDLFEF O27847 17 -1 -
CELEAPEYFRV P71820 17 -1 -

Motif 3 width=13
Element Seqn Id St Int Rpt
VREAARACPVGAI O85696 47 20 -
AKEAAESCPTGAI FER_THELI 44 17 -
AKEAMEACPVSAI FER_PYRFU 49 21 -
VREAATICPAAAI FER2_STRGO 48 21 -
AKDAADSCPTGAI FER_THEMA 44 17 -
CEEAMESCPASAI O30071 44 17 -
AVEAAEACPVSCI Q56300 50 21 -
AQDAIDACPVEAI FER1_DESDN 44 18 -
VEEAMDTCPVQSI FER1_DESAF 47 19 -
VGEAVRACPVGAV FERS_STRGR 48 21 -
ARESVNECPTEAI FER_MOOTH 48 21 -
CGLCEQLCPVDAI O27205 249 16 -
CGLCEQLCPVDAI Q50784 249 16 -
VRLAASQCPVAAI FE45_RHISN 48 21 -
VEDAISTCPVECI FER2_DESVM 46 18 -
MIDAFEGCPTDSI FER_BACSU 54 26 -
AREAGHLCPSGAV FER1_STRGO 49 21 -
CGLCEKLCPTDAI Q49180 248 15 -
MMDAFEGCPTDSI FER_BACTH 54 26 -
IQEAIDTCPVDCI Q55980 89 19 -
VVDSAKECPGECI O87593 72 32 -
MMDAFEGCPTESI FER_BACST 54 26 -
VRLAASQCPVAHS FE45_BRAJA 48 21 -
DAPCANVCPVDAI YSAA_ECOLI 63 20 -
SEKAAGNCPVMCI O27847 54 26 -
IKHAVWACPTQAL P71820 48 20 -