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PR00354

Identifier
7FE8SFRDOXIN  [View Relations]  [View Alignment]  
Accession
PR00354
No. of Motifs
3
Creation Date
11-APR-1995  (UPDATE 09-JUN-1999)
Title
7Fe ferredoxin signature
Database References

PROSITE; PS00198 4FE4S_FERREDOXIN
BLOCKS; BL00198
INTERPRO; IPR000813
PDB; 1FRX
SCOP; 1FRX
CATH; 1FDA
Literature References
1. GEORGE, D.G., HUNT, L.T., YEH, L.S. AND BARKER, W.C.
New perspectives on bacterial ferredoxin evolution.
J.MOL.EVOL. 22 20-31 (1985).
 
2. TROWER, M.K., MARSHALL, J.E., DOLEMAN, M.S., EMPTAGE, M.H. AND 
SARIASLANI, F.S.
Primary structure of a 7Fe ferredoxin from Streptomyces griseus.
BIOCHIM.BIOPHYS.ACTA 1037 290-296 (1990).
 
3. STOUT, C.D.
Refinement of the 7 Fe ferredoxin from Azotobacter vinelandii at 1.9 A 
resolution.
J.MOL.BIOL. 205 545-555 (1989).

Documentation
Ferredoxins [1] are iron-sulphur proteins that mediate electron transfer 
in a range of metabolic reactions. The proteins fall into several subgroups
according to the nature of their iron-sulphur cluster(s). The 7Fe
ferredoxins [2,3] contain both 4Fe-4S and 3Fe-4S centres, which are
spatially related according to the following scheme:
 
                   C  C     C E C
         H2N-------x--x-----x-x-x-----------\
                    \ \    / /  |           |            
                     [3Fe-4S]---' [4Fe-4S]--x C
                         |          / | \   |        
                HOOC-----x---------x--x--x--/
                         C         C  C  C
    
The 4Fe-4S domain is similar to those found in other bacterial-type
ferredoxins.
 
The 3D structure of the 7Fe ferredoxin from Azotobacter vinelandii has been
determined to 1.9 A resolution [3]. 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.
 
7FE8SFRDOXIN is a 3-element fingerprint that provides a signature for 7Fe 
ferredoxins. The fingerprint was derived from an initial alignment of 2 
sequences: motif 1 contains 2 of 3 invariant Cys residues contributing to
the 3Fe-4S cluster, which is located upstream from the 4Fe-4S domain;
motif 2 contains the first invariant Cys of the 4Fe-4S cluster; and motif 3
contains 3 invariant cysteines of the 4Fe-4S cluster and one Cys ligand of
its downstream 3Fe-4S counterpart (see scheme above). Two iterations on
OWL25.1 were required to reach convergence, at which point a true set
comprising 20 sequences was identified. 7 partial matches were also found,
all of them are proteins containing the 4Fe-4S cluster and matching motifs
2 and 3. 
 
An update on SPTR37_9f identified a true set of 16 sequences, and 17
partial matches.
Summary Information
  16 codes involving  3 elements
17 codes involving 2 elements
Composite Feature Index
3161616
201717
123
True Positives
FER1_AZOVI    FER2_RHOCA    FER2_RHORU    FER_ALIAC     
FER_BACSC FER_MYCSM FER_MYCTU FER_PSEPU
FER_PSEST FER_SACER FER_STRGR FER_THETH
O27309 O50433 P96093 Q45972
True Positive Partials
Codes involving 2 elements
FER_BUTME FER_CLOBU FER_CLOPE FER_CLOSP
FER_CLOST FER_CLOTS O26501 O26505
O27205 O27597 O74028 P73649
Q50784 Q57713 Q57934 Q58699
Q59575
Sequence Titles
FER1_AZOVI  FERREDOXIN I (FDI) - AZOTOBACTER VINELANDII.  
FER2_RHOCA FERREDOXIN II (FDII) - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
FER2_RHORU FERREDOXIN II (FDII) - RHODOSPIRILLUM RUBRUM.
FER_ALIAC FERREDOXIN - ALICYCLOBACILLUS ACIDOCALDARIUS (BACILLUS ACIDOCALDARIUS).
FER_BACSC FERREDOXIN 7FE - BACILLUS SCHLEGELII.
FER_MYCSM FERREDOXIN - MYCOBACTERIUM SMEGMATIS.
FER_MYCTU PROBABLE FERREDOXIN - MYCOBACTERIUM TUBERCULOSIS.
FER_PSEPU FERREDOXIN - PSEUDOMONAS PUTIDA.
FER_PSEST FERREDOXIN - PSEUDOMONAS STUTZERI (PSEUDOMONAS PERFECTOMARINA).
FER_SACER FERREDOXIN - SACCHAROPOLYSPORA ERYTHRAEA (STREPTOMYCES ERYTHRAEUS).
FER_STRGR FERREDOXIN - STREPTOMYCES GRISEUS.
FER_THETH FERREDOXIN - THERMUS AQUATICUS (SUBSP. THERMOPHILUS).
O27309 POLYFERREDOXIN - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O50433 FERREDOXIN - MYCOBACTERIUM TUBERCULOSIS.
P96093 FERREDOXIN - THIOBACILLUS FERROOXIDANS.
Q45972 FERREDOXIN A - CAULOBACTER CRESCENTUS.

FER_BUTME FERREDOXIN - BUTYRIBACTERIUM METHYLOTROPHICUM.
FER_CLOBU FERREDOXIN - CLOSTRIDIUM BUTYRICUM.
FER_CLOPE FERREDOXIN - CLOSTRIDIUM PERFRINGENS.
FER_CLOSP FERREDOXIN - CLOSTRIDIUM SP. (STRAIN M-E).
FER_CLOST FERREDOXIN - CLOSTRIDIUM STICKLANDII.
FER_CLOTS FERREDOXIN - CLOSTRIDIUM THERMOSACCHAROLYTICUM (THERMOANAEROBACTERIUM THERMOSACCHAROLYTICUM), AND CLOSTRIDIUM TARTARIVORUM.
O26501 POLYFERREDOXIN - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O26505 POLYFERREDOXIN - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O27205 POLYFERREDOXIN (MVHB) - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O27597 TUNGSTEN FORMYLMETHANOFURAN DEHYDROGENASE, SUBUNIT F - METHANOBACTERIUM THERMOAUTOTROPHICUM.
O74028 TUNGSTEN-CONTAINING FORMYLMETHANOFURAN DEHYDROGENASE ISOENZYME II SUBUNIT F (EC 1.2.99.5) (POLYFERREDOXIN) - METHANOBACTERIUM WOLFEI.
P73649 FERREDOXIN - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
Q50784 FERREDOXIN - METHANOBACTERIUM THERMOAUTOTROPHICUM.
Q57713 HYPOTHETICAL PROTEIN MJ0265 - METHANOCOCCUS JANNASCHII.
Q57934 POLYFERREDOXIN - METHANOCOCCUS JANNASCHII.
Q58699 HYPOTHETICAL PROTEIN MJ1303 - 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
OWL25_1    2  250  NSINGLE    
SPTR37_9f 2 200 NSINGLE
Initial Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
CIKCKYTDCVE FER1_AZOVI 8 8 -
CVDVKDKACIE FER_STRGR 8 8 -

Motif 2 width=11
Element Seqn Id St Int Rpt
EVCPVDCFYEG FER1_AZOVI 18 -1 -
EECPVDCIYEG FER_STRGR 18 -1 -

Motif 3 width=18
Element Seqn Id St Int Rpt
IHPDECIDCALCEPECPA FER1_AZOVI 34 5 -
IHPDECVDCGACEPVCPV FER_STRGR 34 5 -
Final Motifs
Motif 1  width=11
Element Seqn Id St Int Rpt
CIKCKYTDCVE FER1_AZOVI 8 8 -
CIKCKYTDCVE FER_PSEPU 8 8 -
CIKCKYTDCVE FER_PSEST 8 8 -
CIACKYTDCVE FER2_RHOCA 8 8 -
CIKCKYQDCVE FER2_RHORU 8 8 -
CVDVKDKACIE FER_MYCSM 8 8 -
CVDVKDKACIE FER_STRGR 8 8 -
CVRCKFMDCVE Q45972 9 9 -
CVDIKDKACIE O50433 9 9 -
CVDVLDKACIE FER_SACER 8 8 -
CIGTKDASCVE FER_BACSC 8 8 -
CIGVKDQSCVE FER_THETH 8 8 -
CIRCKYTDCVT P96093 9 9 -
CIGEKAADCVE FER_ALIAC 8 8 -
CVDVMDKSCVQ FER_MYCTU 8 8 -
CRDCDETPCIE O27309 269 269 -

Motif 2 width=11
Element Seqn Id St Int Rpt
EVCPVDCFYEG FER1_AZOVI 18 -1 -
EVCPVDCFYEG FER_PSEPU 18 -1 -
EVCPVDCFYEG FER_PSEST 18 -1 -
EVCPVDCFYEG FER2_RHOCA 18 -1 -
EVCPVDCFYEG FER2_RHORU 18 -1 -
EECPVDCIYEG FER_MYCSM 18 -1 -
EECPVDCIYEG FER_STRGR 18 -1 -
EVCPVDCFYEG Q45972 19 -1 -
EECPVDCIYEG O50433 19 -1 -
EECPVDCIYEG FER_SACER 18 -1 -
EVCPVDCIHEG FER_BACSC 18 -1 -
EVCPVECIYDG FER_THETH 18 -1 -
TVCPVDCFHEG P96093 19 -1 -
ETCPVDAIHEG FER_ALIAC 18 -1 -
QECPVDCIYEG FER_MYCTU 18 -1 -
ELCPVDAITLR O27309 336 56 -

Motif 3 width=18
Element Seqn Id St Int Rpt
IHPDECIDCALCEPECPA FER1_AZOVI 34 5 -
IHPDECIDCALCEPECPA FER_PSEPU 34 5 -
IHPDECIDCALCEPECPA FER_PSEST 34 5 -
IHPDECIDCGVCEPECPA FER2_RHOCA 34 5 -
INPDECIDCGVCNPECPA FER2_RHORU 34 5 -
IHPDECVDCGACEPVCPV FER_MYCSM 34 5 -
IHPDECVDCGACEPVCPV FER_STRGR 34 5 -
INPDECIDCGVCEPECPV Q45972 35 5 -
IHPDECVDCGACEPVCPV O50433 35 5 -
IHPDECVDCGACEPVCPV FER_SACER 34 5 -
IDPDVCIDCGACEAVCPV FER_BACSC 34 5 -
IHPEECIDCGACVPACPV FER_THETH 34 5 -
IDPDECIDCTLCVPECPV P96093 35 5 -
IDPDLCIDCAACEPVCPV FER_ALIAC 34 5 -
INPDECVDCGACKPACRV FER_MYCTU 34 5 -
IDPRLCIGCGLCLDVCPE O27309 389 42 -