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PR00256

Identifier
REACTNCENTRE  [View Relations]  [View Alignment]  
Accession
PR00256
No. of Motifs
5
Creation Date
28-FEB-1994  (UPDATE 29-JUL-1999)
Title
Bacterial photosynthetic reaction centre signature
Database References

PROSITE; PS00244 REACTION_CENTER
BLOCKS; BL00244
PFAM; PF00124 photoRC
INTERPRO; IPR000484
PDB; 2RCR
SCOP; 2RCR
CATH; 1PRC
Literature References
1. YOUVAN, D.C., BYLINA, E.J., ALBERTI, M., BEGUSCH, H. AND HEARST, J.E.
Nucleotide and deduced polypeptide sequences of the photosynthetic reaction
center, B870 antenna, and flanking polypeptides from R. capsulata.
CELL 37(3) 949-957 (1984).
 
2. MICHEL, H., WEYER, K.A., GRUENBERG, H., DUNGER, I., OESTERHELT, D. AND
LOTTSPEICH, F.
The light and medium subunits of the photosynthetic reaction center from 
Rhodopseudomonas viridis - Isolation of the genes, nucleotide and amino
acid sequence.
EMBO J. 5(6) 1149-1158 (1986).
 
3. BELANGER, G., BERARO, J., CORRIVEAU, P. AND GINGRAS, G.
The structural genes coding for the L-subunit and M-subunit of
Rhodospirillum rubrum photoreaction center.
J.BIOL.CHEM. 263(16) 7632-7638 (1988).

Documentation
Purple bacteria have a diverse metabolism, which enables them to grow
photosynthetically under anaerobic conditions by virtue of using a
photosynthetic reaction centre (PRC) [1]. Most reaction centres from these
bacteria comprise 3 elements (the light (L), medium (M) and heavy (H)
chains), although some contain a tightly-bound cytochrome molecule [2].
Several other factors, such as carotenoid, bacteriochlorophyll pigments,
quinones and other light-harvesting co-factors are also required [1], all
of which are associated with the L and M chains [3]. The complete complex
is intimately involved in the transformation of light energy into chemical
energy [3], with an adjacent oxidoreductase complex using the reduced
quinones to produce a membrane potential [1]. Many of these processes are
similar to corresponding processes in the thylakoid membranes of higher
plant chloroplasts, which contain photosystem II, a complex similar to the
bacterial PRC [1].
 
The L and M chains are similar polypeptides, which span the membrane and
are required for pigment binding [2,3]. They have been shown to be photo-
chemically active in the absence of the H chain [2]. The PRC is one of the
few transmembrane (TM) complexes for which there is a known structure: it 
has been shown that both the L and M chains have 5 TM helices of between
24-30 amino acids, which are tilted up to 38 degrees to the membrane [2].
A difference in the number and type of charged residues on either side of
the membrane sets up an electrical dipole, which may affect the direction
and speed of the light-driven electron transport effected by the PRC [2].
Although the sequences of the TM regions are not well conserved, L and M
chains contain small clusters of conserved amino acids that correspond to
binding sites for bacteriochlorophyll, iron and quinone [3].
 
REACTNCENTRE is a 5-element fingerprint that provides a signature for the
bacterial PRC L and M chains. The fingerprint was derived from an initial
alignment of 7 sequences: motifs 1-5 encode each of the 5 TM helices -
motif 4 includes most of the region encoded by PROSITE pattern REACTION_
CENTER (PS00244), of which the first and second conserved histidines are
magnesium atom and iron atom ligands respectively. Two iterations on OWL22.0
were required to reach convergence, at which point a true set comprising 14
sequences was identified. Numerous partial matches were also found:
RCEM_CHLAU is a bacterial M chain that fails to make a significant match
with the first motif; the remaining matches constitute a subfamily
of related plant chloroplast photosystem II proteins, all of which match
motifs 2 and 4.   
 
An update on SPTR37_9f identified a true set of 21 sequences, and 11
partial matches.
Summary Information
  21 codes involving  5 elements
4 codes involving 4 elements
0 codes involving 3 elements
7 codes involving 2 elements
Composite Feature Index
52121212121
404444
300000
207520
12345
True Positives
O30843        O30844        O32411        O66386        
O70076 O70105 O82945 O82946
O83005 P95616 RCEL_ERYSP RCEL_RHOCA
RCEL_RHOGE RCEL_RHORU RCEL_RHOSH RCEL_RHOVI
RCEM_RHOCA RCEM_RHOGE RCEM_RHORU RCEM_RHOSH
RCEM_RHOVI
True Positive Partials
Codes involving 4 elements
O32412 RCEL_CHLAU RCEM_CHLAU RCEM_ERYSP
Codes involving 2 elements
PSBA_ECTSI PSBA_PROMA PSBD_CHLRE PSBD_CHLVU
PSBD_EUGGR PSBD_PINTH PSBD_PROHO
Sequence Titles
O30843      REACTION CENTER L SUBUNIT - ECTOTHIORHODOSPIRA SHAPOSHNIKOVII. 
O30844 REACTION CENTER M SUBUNIT - ECTOTHIORHODOSPIRA SHAPOSHNIKOVII.
O32411 PHOTOSYNTHETIC REACTION CENTER L SUBUNIT - RHODOSPIRILLUM MOLISCHIANUM.
O66386 L SUBUNIT OF PHOTOSYNTHETIC REACTION CENTER - ACIDIPHILIUM ACIDOPHILUM.
O70076 M SUBUNIT OF PHOTOSYNTHETIC REACTION CENTER COMPLEX - ACIDIPHILIUM ANGUSTUM, AND ACIDIPHILIUM RUBRUM.
O70105 L SUBUNIT OF PHOTOSYNTHETIC REACTION CENTER COMPLEX - ACIDIPHILIUM ANGUSTUM, AND ACIDIPHILIUM RUBRUM.
O82945 L SUBUNIT OF REACTION CENTER COMPLEX - CHROMATIUM VINOSUM.
O82946 M SUBUNIT OF REACTION CENTER COMPLEX - CHROMATIUM VINOSUM.
O83005 PHOTOSYNTHETIC REACTION CENTER L SUBUNIT - RHODOPSEUDOMONAS PALUSTRIS.
P95616 PHOTOSYNTHETIC REACTION CENTER M SUBUNIT - RHODOCYCLUS GELATINOSUS (RHODOPSEUDOMONAS GELATINOSA).
RCEL_ERYSP REACTION CENTER PROTEIN L CHAIN (PHOTOSYNTHETIC REACTION CENTER L SUBUNIT) - ERYTHROBACTER SP. (STRAIN OCH 114).
RCEL_RHOCA REACTION CENTER PROTEIN L CHAIN (PHOTOSYNTHETIC REACTION CENTER L SUBUNIT) - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
RCEL_RHOGE REACTION CENTER PROTEIN L CHAIN (PHOTOSYNTHETIC REACTION CENTER L SUBUNIT) - RHODOCYCLUS GELATINOSUS (RHODOPSEUDOMONAS GELATINOSA).
RCEL_RHORU REACTION CENTER PROTEIN L CHAIN (PHOTOSYNTHETIC REACTION CENTER L SUBUNIT) - RHODOSPIRILLUM RUBRUM.
RCEL_RHOSH REACTION CENTER PROTEIN L CHAIN (PHOTOSYNTHETIC REACTION CENTER L SUBUNIT) - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
RCEL_RHOVI REACTION CENTER PROTEIN L CHAIN (PHOTOSYNTHETIC REACTION CENTER L SUBUNIT) - RHODOPSEUDOMONAS VIRIDIS.
RCEM_RHOCA REACTION CENTER PROTEIN M CHAIN (PHOTOSYNTHETIC REACTION CENTER M SUBUNIT) - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
RCEM_RHOGE REACTION CENTER PROTEIN M CHAIN (PHOTOSYNTHETIC REACTION CENTER M SUBUNIT) - RHODOCYCLUS GELATINOSUS (RHODOPSEUDOMONAS GELATINOSA).
RCEM_RHORU REACTION CENTER PROTEIN M CHAIN (PHOTOSYNTHETIC REACTION CENTER M SUBUNIT) - RHODOSPIRILLUM RUBRUM.
RCEM_RHOSH REACTION CENTER PROTEIN M CHAIN (PHOTOSYNTHETIC REACTION CENTER M SUBUNIT) - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
RCEM_RHOVI REACTION CENTER PROTEIN M CHAIN (PHOTOSYNTHETIC REACTION CENTER M SUBUNIT) - RHODOPSEUDOMONAS VIRIDIS.

O32412 PHOTOSYNTHETIC REACTION CENTER M SUBUNIT - RHODOSPIRILLUM MOLISCHIANUM.
RCEL_CHLAU REACTION CENTER PROTEIN L CHAIN (PHOTOSYNTHETIC REACTION CENTER L SUBUNIT) - CHLOROFLEXUS AURANTIACUS.
RCEM_CHLAU REACTION CENTER PROTEIN M CHAIN (PHOTOSYNTHETIC REACTION CENTER M SUBUNIT) - CHLOROFLEXUS AURANTIACUS.
RCEM_ERYSP REACTION CENTER PROTEIN M CHAIN (PHOTOSYNTHETIC REACTION CENTER M SUBUNIT) - ERYTHROBACTER SP. (STRAIN OCH 114).

PSBA_ECTSI PHOTOSYSTEM Q(B) PROTEIN (32 KD THYLAKOID MEMBRANE PROTEIN) (PHOTOSYSTEM II PROTEIN D1) - ECTOCARPUS SILICULOSUS.
PSBA_PROMA PHOTOSYSTEM Q(B) PROTEIN (32 KD THYLAKOID MEMBRANE PROTEIN) (PHOTOSYSTEM II PROTEIN D1) - PROCHLOROCOCCUS MARINUS.
PSBD_CHLRE PHOTOSYSTEM II D2 PROTEIN (PHOTOSYSTEM Q(A) PROTEIN) - CHLAMYDOMONAS REINHARDTII.
PSBD_CHLVU PHOTOSYSTEM II D2 PROTEIN (PHOTOSYSTEM Q(A) PROTEIN) - CHLORELLA VULGARIS.
PSBD_EUGGR PHOTOSYSTEM II D2 PROTEIN (PHOTOSYSTEM Q(A) PROTEIN) - EUGLENA GRACILIS.
PSBD_PINTH PHOTOSYSTEM II D2 PROTEIN (PHOTOSYSTEM Q(A) PROTEIN) - PINUS THUNBERGII (GREEN PINE) (JAPANESE BLACK PINE).
PSBD_PROHO PHOTOSYSTEM II D2 PROTEIN (PHOTOSYSTEM Q(A) PROTEIN) - PROCHLOROTHRIX HOLLANDICA.
Scan History
OWL22_0    2  500  NSINGLE    
OWL22_1 1 100 NSINGLE
OWL26_0 1 100 NSINGLE
SPTR37_9f 3 75 NSINGLE
Initial Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
FFGVTTIFFATLGFLLILWGAA RCEL_RHOCA 33 33 -
ASGIAAFAFGSTAILIILFNMA N_1PRCM 53 53 -
FWGFVSVIGIIFGSYFYINETI RCEL_CHLAU 67 67 -
WTSIVAFGTGIAWFVIVGFNML RCEM_ERYSP 58 58 -
FFGVSAIFFIFLGVSLIGYAAS N_1PRCL 33 33 -
WFGNAQLGPIYLGSLGVLSLFS RCEM_RHOSH 41 41 -
FFGVTTLLFTVLGTALIVWGAA RCEL_RHORU 33 33 -

Motif 2 width=29
Element Seqn Id St Int Rpt
GGWYIIASFFLLVSVMTWLLRAYLLAEQH RCEM_ERYSP 115 35 -
GGFWQAITVCALGAFISWMLREVEISRKL N_1PRCL 83 28 -
GGLWLIASFFMFVAVWSWWGRTYLRAQAL RCEM_RHOSH 112 49 -
GGLWQIITFSAIGAFVSWALREVEICRKL RCEL_RHORU 83 28 -
GGLWQVITVCATGAFCSWALREVEICRKL RCEL_RHOCA 83 28 -
GFAWQMTVLFATIAFFGWMMRQVDISMKL RCEL_CHLAU 122 33 -
GGWWLMAGLFMTLSLGSWWIRVYSRARAL N_1PRCM 110 35 -

Motif 3 width=23
Element Seqn Id St Int Rpt
HTAWAFLSAIWLWMVLGFIRPIL RCEM_RHOSH 145 4 -
HVPLAFCVPIFMFCVLQVFRPLL N_1PRCL 116 4 -
HIAWNFAAAIFFVLCIGCIHPTL N_1PRCM 143 4 -
HVPIAFGVAFSAWLVLQVIRPIA RCEL_CHLAU 155 4 -
HIFWGFAAAVWLFLVLGLFRPIL RCEM_ERYSP 148 4 -
HIPVAFSMAIFAYLTLVVIRPMM RCEL_RHOCA 116 4 -
HIPFAFGFAILAYVSLVVIRPVM RCEL_RHORU 116 4 -

Motif 4 width=27
Element Seqn Id St Int Rpt
WHGFSIGFAYGCGLLFAAHGATILAVA N_1PRCM 199 33 -
GHMSSVSFLFVNAMALGLHGGLILSVA N_1PRCL 172 33 -
FHGLSIAFLYGSALLFAMHGATILAVS RCEM_RHOSH 201 33 -
AHMLGITLFFTTCLALALHGSLILSAA RCEL_RHORU 172 33 -
FHMLGISLFFTTAWALAMHGALVLSAA RCEL_RHOCA 172 33 -
FHCLSIVFLYGSVLLFCMHGGTILAVT RCEM_ERYSP 204 33 -
FHAIGITGLFASTWLLACHGSLILSAA RCEL_CHLAU 211 33 -

Motif 5 width=26
Element Seqn Id St Int Rpt
TMEGIHRWAIWMAVLVTLTGGIGILL RCEM_RHOSH 261 33 -
GALSIHRLGLFLASNIFLTGAFGTIA N_1PRCL 225 26 -
TIESVHRWGWFFSLMVMVSASVGILL N_1PRCM 259 33 -
GESGVHRLGYIFAIGGILSADLCILL RCEL_CHLAU 261 23 -
TMEGIHRWAWWFAVLTPITGGIGILL RCEM_ERYSP 264 33 -
GTLGIHRLGLLLALNAVFWSACCMLV RCEL_RHOCA 225 26 -
GTLGIHRVGLILALSAVVWSIICMIL RCEL_RHORU 225 26 -
Final Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
FFGVTTLFFSVLGTALIIWGAS RCEL_RHOGE 33 33 -
FFGVLTAFFALLGTLLIVWGAA O30843 34 34 -
FFGVAGFFFALLGVLLIVWGAT O82945 34 34 -
FFGVTTVFFTLLGVALIVLAAS O32411 34 34 -
FFGVTTIFFATLGFLLILWGAA RCEL_RHOCA 33 33 -
FFGVIGGFFTLLGTALIIWGAA O70105 34 34 -
FFGVTTAFFALLGTILIFWGAS RCEL_ERYSP 34 34 -
FFGVVGGFFTLLGTALIIWGAA O66386 34 34 -
FFGVTTLLFTVLGTALIVWGAA RCEL_RHORU 33 33 -
FFGVTAVFCALMGTALIIWNTA O83005 34 34 -
FFGVATFFFAALGIILIAWSAV RCEL_RHOSH 33 33 -
ALGILSIVFGSLATMIIGFNML P95616 56 56 -
PLGILSIVFGSLAIMIIGFNML RCEM_RHOGE 55 55 -
TTGVLSLVFGFFAIEIIGFNLL RCEM_RHORU 53 53 -
QIGNAQIGPIYLGTLGIASIAT O70076 42 42 -
FTGTLSIIFGFMAIFIIGFNML O82946 55 55 -
WTGLASILFGLMAILIIGFNFL O30844 54 54 -
FFGVSAIFFIFLGVSLIGYAAS RCEL_RHOVI 33 33 -
WFGNAQLGPIYLGSLGVLSLFS RCEM_RHOSH 41 41 -
WMGNAQIGPIYLGIAGTVSLAF RCEM_RHOCA 40 40 -
ASGIAAFAFGSTAILIILFNMA RCEM_RHOVI 53 53 -

Motif 2 width=29
Element Seqn Id St Int Rpt
GGLWQIITVCAIGAFVSWALREVEICRKL RCEL_RHOGE 83 28 -
GGLWQMITICALGAFVSWALRQAEIARKL O30843 84 28 -
GGLWQIITICAIGAFVSWALREVEICRKL O82945 89 33 -
GGFWQFITICATGAFVSWALRQVEIARKL O32411 84 28 -
GGLWQVITVCATGAFCSWALREVEICRKL RCEL_RHOCA 83 28 -
GGLWQIITICAVGSFSSWALREVEISRKL O70105 84 28 -
GGLWQIITICATGAFISWALREVEICRKL RCEL_ERYSP 84 28 -
GGLWQIITICAVGSFGSWALREVEISRKL O66386 84 28 -
GGLWQIITFSAIGAFVSWALREVEICRKL RCEL_RHORU 83 28 -
GGIWQWVTIFATGAFCSWALREVEICRKL O83005 84 28 -
GGLWQIITICATGAFVSWALREVEICRKL RCEL_RHOSH 83 28 -
GGWWLMAGLFLTISILLWWVRMYTRARAL P95616 113 35 -
GGWWLMAGLFLTISILLWWVRMYTRARAL RCEM_RHOGE 112 35 -
GGWWQIAGFFLTTSILLWWVRMYRRARAL RCEM_RHORU 110 35 -
GGWWLMAGFFLTTSLILWWARIYRRSRQL O70076 112 48 -
GGWWLMAGFFLTMSILLWWVRTYKRAEAL O82946 112 35 -
AGWWLMAGFFLTTSILLWWVRMYRRARAW O30844 111 35 -
GGFWQAITVCALGAFISWMLREVEISRKL RCEL_RHOVI 83 28 -
GGLWLIASFFMFVAVWSWWGRTYLRAQAL RCEM_RHOSH 112 49 -
GGVWQIASLFMAISVIAWWVRVYTRADQL RCEM_RHOCA 110 48 -
GGWWLMAGLFMTLSLGSWWIRVYSRARAL RCEM_RHOVI 110 35 -

Motif 3 width=23
Element Seqn Id St Int Rpt
HVPIAFSFAILAYVTLVVIRPIL RCEL_RHOGE 116 4 -
HLPIAFSVAVFAYFTLVVIRPVL O30843 117 4 -
HIPFAFAFAIGAYLVLVVVRPIL O82945 122 4 -
HVPFAFSFAILAYVTLVVIRPVL O32411 117 4 -
HIPVAFSMAIFAYLTLVVIRPMM RCEL_RHOCA 116 4 -
HVPAAFSVAIFAYVTLEVIRPLL O70105 117 4 -
HVPFGFAAAIIAYMTLVIFRPLL RCEL_ERYSP 117 4 -
HVPAAFSVAIFAYVSLEVIRPLL O66386 117 4 -
HIPFAFGFAILAYVSLVVIRPVM RCEL_RHORU 116 4 -
HVPFAFSFAIFAYLTLVVIRPVL O83005 117 4 -
HIPFAFAFAILAYLTLVLFRPVM RCEL_RHOSH 116 4 -
HVAWAFAAAIWLYLVLGFIRPVL P95616 146 4 -
HVAWAFAAAIWLYLVLGFIRPVL RCEM_RHOGE 145 4 -
HTAWAFASAIFLFLSLGFIRPLL RCEM_RHORU 143 4 -
HTAWAFASAIWLYLVLGFIRPLL O70076 145 4 -
HLSWAFAAAIFFYLSLGFIRPVM O82946 145 4 -
HVAWAFAAAIFLYLSLGFFRPIL O30844 144 4 -
HVPLAFCVPIFMFCVLQVFRPLL RCEL_RHOVI 116 4 -
HTAWAFLSAIWLWMVLGFIRPIL RCEM_RHOSH 145 4 -
HMAWAFLSAIWLWSVLGFWRPIL RCEM_RHOCA 143 4 -
HIAWNFAAAIFFVLCIGCIHPTL RCEM_RHOVI 143 4 -

Motif 4 width=27
Element Seqn Id St Int Rpt
AHMLAITFFFTTTLAMSMHGGLILSAA RCEL_RHOGE 172 33 -
AHMLAIAFFFTTALALSLHGGLILSAT O30843 173 33 -
AHMLAITFFFTNCLALSMHGSLILSVT O82945 178 33 -
AHMIAISFFFTNALALAMHGGLILSAS O32411 173 33 -
FHMLGISLFFTTAWALAMHGALVLSAA RCEL_RHOCA 172 33 -
MHMVAVTLFFTTTFALALHGSLVLAAI O70105 173 33 -
AHMLAVTLFFTTTLALALHGGLILSAC RCEL_ERYSP 173 33 -
MHMVAVTLFFTTTFALALHGSLVLGAV O66386 173 33 -
AHMLGITLFFTTCLALALHGSLILSAA RCEL_RHORU 172 33 -
GHMIAITFFFTTCLALALHGGLVLSAI O83005 173 33 -
AHMIAISFFFTNALALALHGALVLSAA RCEL_RHOSH 172 33 -
FHALSIAFLYGATLLFAMHGATILAVS P95616 202 33 -
FHALSIAFLYGATLLFAMHGATILAVS RCEM_RHOGE 201 33 -
FHMLSIAFLYGSALLSAMHGATILAVS RCEM_RHORU 199 33 -
FHMLSIVFLYGSVLLFAMHGATILAVS O70076 201 33 -
FHMLSIAFLYGSALLFAMHGATILAVS O82946 201 33 -
FHMLCIAFLYGSAVLFAMHGATVLAVG O30844 200 33 -
GHMSSVSFLFVNAMALGLHGGLILSVA RCEL_RHOVI 172 33 -
FHGLSIAFLYGSALLFAMHGATILAVS RCEM_RHOSH 201 33 -
FHGLSIAALYGSALLFAMHGATILAVT RCEM_RHOCA 199 33 -
WHGFSIGFAYGCGLLFAAHGATILAVA RCEM_RHOVI 199 33 -

Motif 5 width=26
Element Seqn Id St Int Rpt
GSLGIHRLGLFLALSAAFWSAVCIVI RCEL_RHOGE 225 26 -
GALGIHRLGLFLALSAAFWSAVCIVI O30843 226 26 -
GALAIHRLGLFLALSAVFWSAVCIVI O82945 231 26 -
GALAIHRIGLFLAISAAFWSAVCIVI O32411 226 26 -
GTLGIHRLGLLLALNAVFWSACCMLV RCEL_RHOCA 225 26 -
GTLGIHRLGLFLALGAGFASAACILI O70105 226 26 -
GTLGIHRLGYLLAINAGLWSAICIII RCEL_ERYSP 226 26 -
GTLGIHRLGLFLALGAGFASAACILI O66386 226 26 -
GTLGIHRVGLILALSAVVWSIICMIL RCEL_RHORU 225 26 -
GTIGIHRVGLFLALSAVFWSAVCMLI O83005 226 26 -
GTLGIHRLGLLLSLSAVFFSALCMII RCEL_RHOSH 225 26 -
TTESIHRWAWWFAVLCPLCGGIGILL P95616 262 33 -
TTESIHRWAWWFAVLCPLCGGIGILL RCEM_RHOGE 261 33 -
TMESIHRWAWWFAVLCTFTGAIGILL RCEM_RHORU 259 33 -
TMESIHRWAWWFAVLTTLTGGIGILL O70076 261 33 -
SMESIHRWAWWCAVLTVITAGIGILL O82946 261 33 -
TMESIHRWGWWFAVLVPITGGIGILL O30844 260 33 -
GALSIHRLGLFLASNIFLTGAFGTIA RCEL_RHOVI 225 26 -
TMEGIHRWAIWMAVLVTLTGGIGILL RCEM_RHOSH 261 33 -
TMEGIHRWAIWMAVMVTLTGGIGILL RCEM_RHOCA 259 33 -
TIESVHRWGWFFSLMVMVSASVGILL RCEM_RHOVI 259 33 -