ARFA_MYCTU
ID ARFA_MYCTU Reviewed; 326 AA.
AC P9WIU5; L0T818; P65593; Q10557;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 38.
DE RecName: Full=Peptidoglycan-binding protein ArfA;
DE AltName: Full=Outer membrane porin A;
DE AltName: Full=Outer membrane protein A;
DE Short=OmpATb;
DE AltName: Full=Outer membrane protein ArfA;
GN Name=arfA; Synonyms=ompA; OrderedLocusNames=Rv0899; ORFNames=MTCY31.27;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=12366842; DOI=10.1046/j.1365-2958.2002.03152.x;
RA Raynaud C., Papavinasasundaram K.G., Speight R.A., Springer B., Sander P.,
RA Bottger E.C., Colston M.J., Draper P.;
RT "The functions of OmpATb, a pore-forming protein of Mycobacterium
RT tuberculosis.";
RL Mol. Microbiol. 46:191-201(2002).
RN [3]
RP FUNCTION AS A CHANNEL, SUBCELLULAR LOCATION, NON-CLEAVABLE SIGNAL SEQUENCE,
RP AND SUBUNIT.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=17573469; DOI=10.1128/jb.00509-07;
RA Alahari A., Saint N., Campagna S., Molle V., Molle G., Kremer L.;
RT "The N-terminal domain of OmpATb is required for membrane translocation and
RT pore-forming activity in mycobacteria.";
RL J. Bacteriol. 189:6351-6358(2007).
RN [4]
RP SUBCELLULAR LOCATION.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=18439872; DOI=10.1016/j.tube.2008.02.004;
RA Song H., Sandie R., Wang Y., Andrade-Navarro M.A., Niederweis M.;
RT "Identification of outer membrane proteins of Mycobacterium tuberculosis.";
RL Tuberculosis 88:526-544(2008).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [6]
RP FUNCTION IN AMMONIA SECRETION, INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21410778; DOI=10.1111/j.1365-2958.2011.07619.x;
RA Song H., Huff J., Janik K., Walter K., Keller C., Ehlers S., Bossmann S.H.,
RA Niederweis M.;
RT "Expression of the ompATb operon accelerates ammonia secretion and
RT adaptation of Mycobacterium tuberculosis to acidic environments.";
RL Mol. Microbiol. 80:900-918(2011).
RN [7]
RP STRUCTURE BY NMR OF 73-203, AND SUBUNIT.
RX PubMed=20199110; DOI=10.1021/bi100158s;
RA Teriete P., Yao Y., Kolodzik A., Yu J., Song H., Niederweis M.,
RA Marassi F.M.;
RT "Mycobacterium tuberculosis Rv0899 adopts a mixed alpha/beta-structure and
RT does not form a transmembrane beta-barrel.";
RL Biochemistry 49:2768-2777(2010).
RN [8]
RP STRUCTURE BY NMR OF 52-326, SUBUNIT, DISULFIDE BOND, AND PUTATIVE
RP ZINC-BINDING.
RX PubMed=22108166; DOI=10.1016/j.jmb.2011.11.016;
RA Li J., Shi C., Gao Y., Wu K., Shi P., Lai C., Chen L., Wu F., Tian C.;
RT "Structural studies of Mycobacterium tuberculosis Rv0899 reveal a monomeric
RT membrane-anchoring protein with two separate domains.";
RL J. Mol. Biol. 415:382-392(2012).
RN [9]
RP STRUCTURE BY NMR OF 196-326, DISULFIDE BOND, PEPTIDOGLYCAN-BINDING, AND
RP MUTAGENESIS OF LEU-232; ASP-236 AND ARG-277.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=22206986; DOI=10.1016/j.jmb.2011.12.030;
RA Yao Y., Barghava N., Kim J., Niederweis M., Marassi F.M.;
RT "Molecular structure and peptidoglycan recognition of Mycobacterium
RT tuberculosis ArfA (Rv0899).";
RL J. Mol. Biol. 416:208-220(2012).
RN [10]
RP STRUCTURE BY NMR OF 73-204 AND OF 198-326, DISULFIDE BOND, AND SUBUNIT.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21117233; DOI=10.1002/prot.22912;
RA Yang Y., Auguin D., Delbecq S., Dumas E., Molle G., Molle V.,
RA Roumestand C., Saint N.;
RT "Structure of the Mycobacterium tuberculosis OmpATb protein: a model of an
RT oligomeric channel in the mycobacterial cell wall.";
RL Proteins 79:645-661(2011).
CC -!- FUNCTION: Probably plays a role in ammonia secretion that neutralizes
CC the medium at pH 5.5, although it does not play a direct role in
CC ammonia transport. The OmpA-like domain (196-326) binds M.tuberculosis
CC peptidoglycan. Overexpression in M.bovis or M.smegmatis gives channels
CC with average conductance value of 1,600 +/- 100 pS, but this may not be
CC physiologically relevant. {ECO:0000269|PubMed:12366842,
CC ECO:0000269|PubMed:17573469, ECO:0000269|PubMed:21410778}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Note=May bind Zn(2+) via residues in the BON domain.;
CC -!- SUBUNIT: Controversial; may form oligomers (PubMed:17573469,
CC PubMed:21117233), or not (PubMed:20199110, PubMed:21117233).
CC {ECO:0000269|PubMed:17573469, ECO:0000269|PubMed:20199110,
CC ECO:0000269|PubMed:21117233, ECO:0000269|PubMed:22108166}.
CC -!- SUBCELLULAR LOCATION: Secreted, cell wall. Cell outer membrane.
CC Note=Does not have a cleavable signal sequence.
CC -!- INDUCTION: Induced at low pH (at protein level), upon infecting a human
CC monocytic cell line and in murine bone marrow macrophages. Part of the
CC arfA-arfB-arfC operon. Maximal expression of ArfA requires the full
CC operon. {ECO:0000269|PubMed:12366842, ECO:0000269|PubMed:21410778}.
CC -!- DISRUPTION PHENOTYPE: Significantly impaired growth at pH 5.5, reduced
CC uptake of serine at both pH 7.2 and 5.5. Reduces growth in macrophages
CC and in intravenously infected mice (PubMed:12366842). But the same
CC mutant has very little effect when studied by another group
CC (PubMed:21410778). Upon operon disruption no reduction of serine uptake
CC at pH 6.9, no visible effect on outer membrane permeability, however
CC severe delays in ammonia secretion, medium pH neutralization and growth
CC also occur at pH 5.5 (PubMed:21410778). {ECO:0000269|PubMed:12366842,
CC ECO:0000269|PubMed:21410778}.
CC -!- SIMILARITY: Belongs to the outer membrane OOP (TC 1.B.6) superfamily.
CC ArfA family. {ECO:0000305}.
CC -!- CAUTION: Was originally thought to be a porin.
CC {ECO:0000305|PubMed:12366842}.
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DR EMBL; AL123456; CCP43647.1; -; Genomic_DNA.
DR PIR; H70782; H70782.
DR RefSeq; NP_215414.1; NC_000962.3.
DR RefSeq; WP_003404684.1; NZ_NVQJ01000001.1.
DR PDB; 2KGS; NMR; -; A=73-204.
DR PDB; 2KGW; NMR; -; A=198-326.
DR PDB; 2KSM; NMR; -; A=73-203.
DR PDB; 2L26; NMR; -; A=52-326.
DR PDB; 2LBT; NMR; -; A=196-326.
DR PDB; 2LCA; NMR; -; A=196-326.
DR PDBsum; 2KGS; -.
DR PDBsum; 2KGW; -.
DR PDBsum; 2KSM; -.
DR PDBsum; 2L26; -.
DR PDBsum; 2LBT; -.
DR PDBsum; 2LCA; -.
DR AlphaFoldDB; P9WIU5; -.
DR BMRB; P9WIU5; -.
DR SMR; P9WIU5; -.
DR STRING; 83332.Rv0899; -.
DR PaxDb; P9WIU5; -.
DR DNASU; 885286; -.
DR GeneID; 885286; -.
DR KEGG; mtu:Rv0899; -.
DR TubercuList; Rv0899; -.
DR eggNOG; COG2885; Bacteria.
DR OMA; MKGEVHN; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0009279; C:cell outer membrane; IDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; IDA:MTBBASE.
DR GO; GO:0005576; C:extracellular region; IEA:UniProtKB-KW.
DR GO; GO:0005887; C:integral component of plasma membrane; HDA:MTBBASE.
DR GO; GO:0009274; C:peptidoglycan-based cell wall; HDA:MTBBASE.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0042834; F:peptidoglycan binding; IDA:MTBBASE.
DR GO; GO:0015288; F:porin activity; IDA:MTBBASE.
DR GO; GO:0072488; P:ammonium transmembrane transport; IDA:MTBBASE.
DR GO; GO:0010447; P:response to acidic pH; IDA:MTBBASE.
DR GO; GO:0075293; P:response to host pH environment; IMP:GO_Central.
DR CDD; cd07185; OmpA_C-like; 1.
DR Gene3D; 3.30.1330.60; -; 1.
DR InterPro; IPR007055; BON_dom.
DR InterPro; IPR006664; OMP_bac.
DR InterPro; IPR006665; OmpA-like.
DR InterPro; IPR006690; OMPA-like_CS.
DR InterPro; IPR036737; OmpA-like_sf.
DR Pfam; PF04972; BON; 1.
DR Pfam; PF00691; OmpA; 1.
DR PRINTS; PR01021; OMPADOMAIN.
DR SUPFAM; SSF103088; SSF103088; 1.
DR PROSITE; PS01068; OMPA_1; 1.
DR PROSITE; PS51123; OMPA_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell outer membrane; Cell wall; Disulfide bond;
KW Ion transport; Membrane; Metal-binding; Reference proteome; Secreted;
KW Transmembrane; Transmembrane helix; Transport; Zinc.
FT CHAIN 1..326
FT /note="Peptidoglycan-binding protein ArfA"
FT /id="PRO_0000196259"
FT TRANSMEM 30..50
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 127..196
FT /note="BON"
FT DOMAIN 212..326
FT /note="OmpA-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00473"
FT REGION 1..73
FT /note="Required for protein translocation to the outer
FT membrane"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..20
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT DISULFID 208..250
FT /evidence="ECO:0000269|PubMed:21117233,
FT ECO:0000269|PubMed:22108166, ECO:0000269|PubMed:22206986"
FT MUTAGEN 232
FT /note="L->G: Decreases structure stability of OmpA-like
FT domain."
FT /evidence="ECO:0000269|PubMed:22206986"
FT MUTAGEN 236
FT /note="D->A: Increases conformational stability of OmpA-
FT like domain. Does not alter peptidoglycan-binding."
FT /evidence="ECO:0000269|PubMed:22206986"
FT MUTAGEN 277
FT /note="R->E: Loss of peptidoglycan-binding; in association
FT with A236."
FT /evidence="ECO:0000269|PubMed:22206986"
FT STRAND 79..86
FT /evidence="ECO:0007829|PDB:2KGS"
FT STRAND 88..98
FT /evidence="ECO:0007829|PDB:2KGS"
FT HELIX 100..111
FT /evidence="ECO:0007829|PDB:2KGS"
FT STRAND 119..122
FT /evidence="ECO:0007829|PDB:2KGS"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:2KGS"
FT HELIX 139..145
FT /evidence="ECO:0007829|PDB:2KGS"
FT STRAND 152..157
FT /evidence="ECO:0007829|PDB:2KGS"
FT STRAND 159..163
FT /evidence="ECO:0007829|PDB:2KGS"
FT STRAND 165..168
FT /evidence="ECO:0007829|PDB:2KGS"
FT HELIX 169..182
FT /evidence="ECO:0007829|PDB:2KGS"
FT STRAND 186..190
FT /evidence="ECO:0007829|PDB:2KGS"
FT STRAND 195..198
FT /evidence="ECO:0007829|PDB:2KSM"
FT STRAND 200..202
FT /evidence="ECO:0007829|PDB:2KGW"
FT STRAND 206..208
FT /evidence="ECO:0007829|PDB:2KGW"
FT HELIX 211..219
FT /evidence="ECO:0007829|PDB:2KGW"
FT STRAND 223..225
FT /evidence="ECO:0007829|PDB:2L26"
FT TURN 227..230
FT /evidence="ECO:0007829|PDB:2LBT"
FT HELIX 234..248
FT /evidence="ECO:0007829|PDB:2KGW"
FT STRAND 255..259
FT /evidence="ECO:0007829|PDB:2KGW"
FT HELIX 267..288
FT /evidence="ECO:0007829|PDB:2KGW"
FT HELIX 292..294
FT /evidence="ECO:0007829|PDB:2KGW"
FT STRAND 295..299
FT /evidence="ECO:0007829|PDB:2KGW"
FT STRAND 309..311
FT /evidence="ECO:0007829|PDB:2L26"
FT HELIX 312..318
FT /evidence="ECO:0007829|PDB:2KGW"
FT STRAND 321..325
FT /evidence="ECO:0007829|PDB:2KGW"
SQ SEQUENCE 326 AA; 33574 MW; 9E0D46ABCC179F4A CRC64;
MASKAGLGQT PATTDARRTQ KFYRGSPGRP WLIGAVVIPL LIAAIGYGAF ERPQSVTGPT
GVLPTLTPTS TRGASALSLS LLSISRSGNT VTLIGDFPDE AAKAALMTAL NGLLAPGVNV
IDQIHVDPVV RSLDFSSAEP VFTASVPIPD FGLKVERDTV TLTGTAPSSE HKDAVKRAAT
STWPDMKIVN NIEVTGQAPP GPPASGPCAD LQSAINAVTG GPIAFGNDGA SLIPADYEIL
NRVADKLKAC PDARVTINGY TDNTGSEGIN IPLSAQRAKI VADYLVARGV AGDHIATVGL
GSVNPIASNA TPEGRAKNRR VEIVVN
