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Amino Acid Sequences of Bacterial Cytochromes C' and C-556 (Bacterial Evolution/Heme Ligands/Protein Structure) R

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Amino Acid Sequences of Bacterial Cytochromes C' and C-556 (Bacterial Evolution/Heme Ligands/Protein Structure) R Proc. NatL Acad. Sci. USA Vol. 78, No. 11, pp. 6854-6857, November 1981 Biochemistry Amino acid sequences of bacterial cytochromes c' and c-556 (bacterial evolution/heme ligands/protein structure) R. P. AMBLER*, R. G. BARTSCHt, M. DANIEL*, M. D. KAMENtt, L. MCLELLAN*, T. E. MEYERt, AND J. VAN BEEUMEN§ *Department of Molecular Biology, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, Scotland; tDepartment of Chemistry A-002, University of California at San Diego, La Jolla, California 92093; and §Laboratory for Microbiology and Microbial Genetics, University of Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium Contributed by Martin D. Kamen, August 20, 1981 ABSTRACT The cytochromes c' are electron transport pro- chrome c' was eluted together with nucleic acid with 0.5 M teins widely distributed in photosynthetic and aerobic bacteria. sodium chloride when the column was developed with a linear We report the amino acid sequences of the proteins from 12 dif- gradient offrom 0.1 to 0.6 M NaCl in 0.02 M Tris HCl, pH 7.3. ferent bacterial species, and we show by sequences that the cy- The cytochrome c' was then precipitated with ammonium sul- tochromes c-556 from 2 different bacteria are structurally related fate (70-100% saturation fraction) and subjected to gel filtration to the cytochromes c'. Unlike the mitochondrial cytochromes c, through Sephadex G-75. The cytochrome c' was then adsorbed the heme binding site in the cytochromes c' and c-556 is near the to hydroxylapatite and eluted with approximately 0.16 M phos- COOH terminus. The cytochromes c-556 probably have a methi- onine sixth heme ligand located near the NH2 terminus, whereas phate when a linear gradient offrom 0 to 0.2 M potassium phos- the cytochromes c' may be pentacoordinate. Quantitative com- phate, pH 7.0, in 0.2 M NaCl was used. Final purification was parison ofcytochrome c' and c-556 sequences indicates a relatively achieved by repetition of the hydroxylapatite and DEAE-cel- low 28% average identity. lulose chromatography, with yields of about 5 1Lmol/kg ofwet cells. The preparation and properties ofthe Agrobacterium tu- mefaciens cytochrome c-556 has been reported by Van Beeu- The cytochromes c' constitute a class ofelectron transport pro- men et al. (9). teins that are widely distributed in phototrophic and aerobic bacteria (1). The heme is covalently bound to cysteine residues, so the proteins are classed as cytochromes c although there is RESULTS AND DISCUSSION little further similarity in properties and structure to the well- The evidence for the amino acid sequences ofthe cytochromes characterized cytochrome c of mitochondria. Thus the cyto- c' fromAlcaligenes sp. National Collection ofIndustrial Bacteria chromes c' heme is in a high-spin environment, similar to that (NCIB) 11015 (10), Rhodospirillum rubrum (11), and Chro- in the globins, but is unreactive with most common heme li- matium vinosum (12) has already been published, and the se- gands, with the exception ofnitric oxide and carbon monoxide. quences of the Rhodopseudomonas gelatinosa and Rhodospi- The tertiary structure of one of the cytochromes c' has been rillum tenue (13) andAgrobacterium tumefaciens strain B2a (14) determined (2, 3), and it shows that there is no relationship proteins have been reported. The additional sequences shown between the overall folding patterns ofcytochromes c' and the in Fig. 1 have been determined by similar methods, and to sim- mitochondrial cytochrome c family (4). The cytochromes c' do ilar standards, as described by Ambler et aL (12). show a fortuitous or distant similarity in folding pattern to Esch- The sequences shown in Fig. 1 include those ofproteins from erichia coli cytochrome b-562, ferritin, and hemerythrin (5). We 9 of the 12 species of Rhodospirillaceae described by Pfennig have determined the amino acid sequences of cytochromes c' and Truper in the 8th edition ofBergey's Manual (16). We find from 10 species of phototrophic bacteria and from 2 very dif- that the protein is absent (or expressed only at very low levels) ferent denitrifying bacteria. There are some structural features from the other three species, Rhodopseudomonas viridis, Rho- common to all the proteins, but the sequences are so divergent dopseudomonas acidophila, and Rhodomicrobium vannielii (1), that choice ofalignments is equivocal. We have also determined and also from the recently described Rhodopseudomonas glob- the amino acid sequences of low-spin cytochromes c-556 from iformis (17). Cytochrome c' is present in most of the strains of a photosynthetic and from an aerobic bacterium, and we dis- Rhodopseudomonas palustris that we have examined, but is cover that, despite spectral differences, the proteins are struc- apparently absent from the neotype strain 2.1.6 (ATCC 17001), turally very similar to cytochromes c'. although no photosynthetic or respiratory anomalies have been noticed in this strain. Cytochrome c' is present in Azotobacter MATERIALS AND METHODS vinelandii (18), Alcaligenes faecalis (unpublished results), and General methods for the isolation of cytochrome c' from pho- Methylococcus capsulatus (unpublished results). tosynthetic bacteria have been described by Bartsch (6). The Rhodopseudomonas palustris synthesizes a low-spin cyto- cytochrome c' from the halophilic "Micrococcus" American chrome c with an a band absorption maximum at 556 nm (1). Type Culture Collection (ATCC) 12084 [which should be pro- Spectrally similar cytochromes c-556 have also been found in visionally assigned to the genus Paracoccus (7)] was described Rhodopseudonnnas sulphidophila (19) by Bartsch (1), and in as a hydroxylamine reductase by Kono and Taniguchi (8). We various strains of the nonphotosynthetic bacterium Agrobac- prepared a cell extract as described by Tedro et aL (7) and ad- terium tumefaciens (9). The sequences of two proteins of this sorbed the colored proteins onto DEAE-cellulose. The cyto- type have been determined (Fig. 1 and ref. 14), and they clearly resemble the cytochromes c' (20) in having the heme attach- The publication costs ofthis article were defrayed in part by page charge ment site close to the COOH terminus. payment. This article must therefore be hereby marked "advertise- ment" in accordance with 18 U. S. C. §1734 solely to indicate this fact. t To whom reprint requests should be addressed. 6854 Downloaded by guest on September 28, 2021 Biochemistry: Ambler et aL Proc. Natd Acad. Sci. USA 78 (1981) 6855 helix A H helix B-J helix C Hhelix D-j 12 16 58 70 76 82 125 (A) QQSKPEDLLKLRQGLMQTLKSQWVPIAGFAAGKADLPADAAQRAEMLAMVAKLA--PI-GWAKGTEA-LPNG-ETKPE-AFGSKSAEFLEGWKALATESTKLAAAAKAG-PDALKAQAAATGKVCKACHEEFKQD I~ ~~~~~~~~II1 ~ ~1 ~ ~~~ ~ ~~~1111PII1 (B) QQSKPEELLKLRQGLtuTLKSQWAPIAGFAAGKADLPADAAQRAENMVLVAKLA--PI-GWAKGTEA-LPNS-ETKAE-AFGARGAMESLAAKAGPDALKAQAAATGRVCKACHEEFKQD l I II 1111 11 (C) AEPEDAIHYRQSALSVMGWQMGPMGAMAQG zIDADEFATRANNAVAH-LPWEGFTEGTLQGDDHGVETDALADIGDDWEGFEERQETFKQEAATLAQMDDGEEFSALRRQVGAVGKSCKGCHDDFRAE l I 1111 11 (D) EPAKSEDLIKWRQSAYQVLHWNMDRLKANIDSPQYNKDDGIKAANTIAAIANSG-W GSLFAAGTETGKGWH-PTSVKPAFFTDGKKVGEVANKNEKVAATG-DAAAVKAQFGKVGQTCKACHDDFRRKDII (E) AGLSPEEQIETRQAGYEFFWNGKIKANLEG-EYNAAQVEANVAIANS G-G-ALYGPGTDKNVGDV-KTRVKPEFFQNMEDVGKIAREFVGAATAVAATG-EAEAVKTAFGDVGAACKSCHEKYRAK (F) QFQKPGDAIEYRQSAFTLIANHFGRVAAMA4G-KAPFDAKVAAENIALVSTLSK-LPLTAFGPGTDKGHG---TEAKPAVWSDAAGFAAA LDKMAVDLGKTG-DFAQIKAAVGETGGACKGCHDKFKEK (G) QFAKPEDAVKYRQSALTLMASHFGRMTPVvKG-QAPYDMAQIKANVEVLKTLSA-LPWAAFGPGTE-GGD---ARPEIWSDAASFKQKQQAFQDNIVKLSAAADAG-DLDKLRAAFGDVGASCKACHDAYRKKK I~~~~~II1 ~~ ~~ ~~~ ~ ~ ~~~~~1 11 11 11 (H)(C)~wew -w--Pw-aADAEHVVEARKGYFSLVALEFGPLAAMAKG-EMriD^AAAHASDLVTLTKYDPSDLYAPGTSADDVKG--TAAKAAIWQDADGFQAKGMLAFFEAVAALEPAAGAG--QKELAAAVGKVGTGCKSCHDDFRVKR s -^AA-vVsttY~w svn~n~r~nmr (I) ADTKEVLEAREAYFKSLGKSNKAMTGVAK-SFDAEAAKAEAAALEKIATD-VA-PLFPAGTSSTDLPG-QTEAKAAIWTNMADFG;AKGKMNDHJAGAEVLAAANA DATAGLQKLGLGTC.KAHLDDLlYKR!EJ (J) DGMETVKARQDYFKSLGGAIKALSGVAK--NYDAEAAKAEAKLEAILATD-IK-PLFAPGTSDADFPG-ESEAKASIWENMEDFGAKGQAMHEAGMELIAAANITG-EASAFGPALKKLGGTCKACHDDYRAEH l~~~~l 11 ~ ~ ~1 ~~1 ~ ~ ~~ ~ ~~~~~l 11 11 11 (K) ADPAAYVEYRKSVLSATSNYFKAIGITLKE-DLAVPNQTADHAKAIASIMET-LP-AAFPEGTAGIAK---TEAKAAIWKDFEAFKVASKKSQDAALELASAAET1( -DKAAIGAKLQALGGTCKACHKEFKAD ASPEAYVEYRKQALKASGDHMKALSAIVKG-QLPLNAEAAHEAIAAIMES-LP-AAFPEGTAGIAK---TEAKAVVWSKADEFKADAVKSADAAKALAQAATAG-DTA~MGKALAALGGTCKGCHETFRE (L) Ij11 l l l11 11 (M) AGEVEKREGMM-KQIGGAMGSLAAISKG~-ER.&FDADTVKAAVTTIGTNAKAFP-EQFPAGTETG---SAAAPAIWENFEDFKAKAAKLGTDADIVLANLPDL,-Q~AGvATAM-KTLGADCGTCHQTYRIKK I ~~~~~~~~~I~ ~ 1 11 11 (N) QQDLVDKTQKLMKDNGRNMMVLGAIAKG-EKPYDQAAVDAALKQFDETAKDLP-KLFPDSVKGLKPFDSKYSSSPKIWAERAKFDTEIADFAKAVDGAKGKIK---DVDTLKAAMQPIGKACGNCHENFRDKEG ll l l 11111 (0) QTDIAQKALKQGETKPAAlKG-ju'DAVQKLAAADSKLPALPASKTGD--AAPKWEKAKDDFALAAAAQTDVIQRKALKQMEATRIMMLG-EA~VQAWKSLAIADDKKLPALFPASKTGl)--AALPIWEDAKFDDFAKLAAATAQGTK -DASLKAIGGVGNCKCHDDRAKK FIG. 1. Amino acid sequences of bacterial cytochromes c' (A-L and 0) and c-556 (M and N). Residues are numbered from the R. molischianum sequence, for which the tertiary structure is known (2, 3), and the extent of the a helices in this protein are indicated (5). Insertions and deletions have been positioned so as to emphasize conserved residues of possible structural significance (see the text), which are indicated by vertical bars between the sequences. The sequences are from: (A)R. molischianum strain S (ATCC 14031), (B)R.fulvumstrain 1360 (ATCC 15798), (C)Paracoccus sp. (ATCC 12084), (D) R. tenue strain 3761, (E) Chromatium vinosum strain D (ATCC 17899), (F)Rhodopseudomonasgelatinosa
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