P65593 (ARFA_MYCTU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Peptidoglycan-binding protein ArfA

Alternative name(s):
Outer membrane porin A
Outer membrane protein A
Short name=OmpATb
Outer membrane protein ArfA

Gene names

Name:	arfA
Synonyms:	ompA
Ordered Locus Names:	Rv0899, MT0922
ORF Names:	MTCY31.27

Organism

Mycobacterium tuberculosis [Reference proteome] [HAMAP]

Taxonomic identifier

1773 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Actinobacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Mycobacteriaceae › Mycobacterium › Mycobacterium tuberculosis complex

Protein attributes

Sequence length	326 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Probably plays a role in ammonia secretion that neutralizes the medium at pH 5.5, although it does not play a direct role in ammonia transport. The OmpA-like domain (196-326) binds M.tuberculosis peptidoglycan. Overexpression in M.bovis or M.smegmatis gives channels with average conductance value of 1,600 +/- 100 pS, but this may not be physiologically relevant. Ref.3 Ref.4 Ref.6
Cofactor	May bind Zn2+ via residues in the BON domain.
Subunit structure	Controversial; may form oligomers (Ref.4, Ref.10), or not (Ref.7, Ref.10). Ref.4 Ref.7 Ref.8 Ref.10
Subcellular location	Secreted › cell wall. Cell outer membrane. Note: Does not have a cleavable signal sequence. Ref.4 Ref.5
Induction	Induced at low pH (at protein level), upon infecting a human monocytic cell line and in murine bone marrow macrophages. Part of the arfA-arfB-arfC operon. Maximal expression of ArfA requires the full operon. Ref.3 Ref.6
Disruption phenotype	Significantly impaired growth at pH 5.5, reduced uptake of serine at both pH 7.2 and 5.5. Reduces growth in macrophages and in intravenously infected mice (Ref.3). But the same mutant has very little effect when studied by another group (Ref.6). Upon operon disruption no reduction of serine uptake at pH 6.9, no visible effect on outer membrane permeability, however severe delays in ammonia secretion, medium pH neutralization and growth also occur at pH 5.5 (Ref.6). Ref.3 Ref.6
Sequence similarities	Belongs to the OmpA family. ArfA(Rv0899) subfamily. Contains 1 BON domain. Contains 1 OmpA-like domain.
Caution	Was originally thought to be a porin (Ref.3).

Ontologies

Keywords
Biological process	Ion transport Transport
Cellular component	Cell membrane Cell outer membrane Cell wall Membrane Secreted
Domain	Transmembrane Transmembrane helix
Ligand	Metal-binding Zinc
PTM	Disulfide bond
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	ammonium transmembrane transport Inferred from direct assay Ref.6. Source: MTBBASE growth of symbiont in host organelle Inferred from mutant phenotype Ref.3. Source: MTBBASE response to acidity Inferred from direct assay Ref.6. Source: MTBBASE
Cellular_component	cell outer membrane Inferred from direct assay Ref.5. Source: UniProtKB cell wall Inferred from direct assay PubMed 20825248. Source: MTBBASE cytosol Inferred from direct assay PubMed 11967065. Source: MTBBASE extracellular region Inferred from electronic annotation. Source: UniProtKB-KW integral to plasma membrane Inferred from direct assay PubMed 15952732. Source: MTBBASE
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW peptidoglycan binding Inferred from direct assay Ref.9. Source: UniProtKB porin activity Inferred from direct assay PubMed 16803587PubMed 9657995. Source: MTBBASE
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 326

326

Peptidoglycan-binding protein ArfA

PRO_0000196259

Regions

Transmembrane

30 – 50

21

Helical; Potential

Domain

127 – 196

70

BON

Domain

212 – 326

115

OmpA-like

Region

1 – 73

73

Required for protein translocation to the outer membrane

Amino acid modifications

Disulfide bond

208 ↔ 250

Ref.8 Ref.9 Ref.10

Experimental info

Mutagenesis

232

1

L → G: Decreases structure stability of OmpA-like domain. Ref.9

Mutagenesis

236

1

D → A: Increases conformational stability of OmpA-like domain. Does not alter peptidoglycan-binding. Ref.9

Mutagenesis

277

1

R → E: Loss of peptidoglycan-binding; in association with A236. Ref.9

Secondary structure

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326

Helix Strand Turn

Details...

Beta strand

79 – 86

8

Beta strand

88 – 98

11

Helix

100 – 111

12

Beta strand

119 – 122

4

Helix

135 – 137

3

Helix

139 – 145

7

Beta strand

152 – 157

6

Beta strand

159 – 163

5

Beta strand

165 – 168

4

Helix

169 – 182

14

Beta strand

186 – 190

5

Beta strand

195 – 198

4

Beta strand

200 – 202

3

Beta strand

206 – 208

3

Helix

211 – 219

9

Beta strand

223 – 225

3

Turn

227 – 230

4

Helix

234 – 248

15

Beta strand

255 – 259

5

Helix

267 – 288

22

Helix

292 – 294

3

Beta strand

295 – 299

5

Beta strand

309 – 311

3

Helix

312 – 318

7

Beta strand

321 – 325

5

Sequences

	Sequence		Length	Mass (Da)
	P65593 [UniParc]. Last modified October 11, 2004. Version 1. Checksum: 9E0D46ABCC179F4A	FASTA	326	33,574
	10 20 30 40 50 60 MASKAGLGQT PATTDARRTQ KFYRGSPGRP WLIGAVVIPL LIAAIGYGAF ERPQSVTGPT 70 80 90 100 110 120 GVLPTLTPTS TRGASALSLS LLSISRSGNT VTLIGDFPDE AAKAALMTAL NGLLAPGVNV 130 140 150 160 170 180 IDQIHVDPVV RSLDFSSAEP VFTASVPIPD FGLKVERDTV TLTGTAPSSE HKDAVKRAAT 190 200 210 220 230 240 STWPDMKIVN NIEVTGQAPP GPPASGPCAD LQSAINAVTG GPIAFGNDGA SLIPADYEIL 250 260 270 280 290 300 NRVADKLKAC PDARVTINGY TDNTGSEGIN IPLSAQRAKI VADYLVARGV AGDHIATVGL 310 320 GSVNPIASNA TPEGRAKNRR VEIVVN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence." Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K. , Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S., Barrell B.G. Nature 393:537-544(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 25618 / H37Rv.
[2]	"Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains." Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O., Peterson J.D., DeBoy R.T., Dodson R.J., Gwinn M.L., Haft D.H., Hickey E.K., Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D., Salzberg S.L., Delcher A., Utterback T.R. , Weidman J.F., Khouri H.M., Gill J., Mikula A., Bishai W., Jacobs W.R. Jr., Venter J.C., Fraser C.M. J. Bacteriol. 184:5479-5490(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CDC 1551 / Oshkosh.
[3]	"The functions of OmpATb, a pore-forming protein of Mycobacterium tuberculosis." Raynaud C., Papavinasasundaram K.G., Speight R.A., Springer B., Sander P., Bottger E.C., Colston M.J., Draper P. Mol. Microbiol. 46:191-201(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INDUCTION, DISRUPTION PHENOTYPE. Strain: ATCC 25618 / H37Rv.
[4]	"The N-terminal domain of OmpATb is required for membrane translocation and pore-forming activity in mycobacteria." Alahari A., Saint N., Campagna S., Molle V., Molle G., Kremer L. J. Bacteriol. 189:6351-6358(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A CHANNEL, SUBCELLULAR LOCATION, NON-CLEAVABLE SIGNAL SEQUENCE, SUBUNIT. Strain: ATCC 25618 / H37Rv.
[5]	"Identification of outer membrane proteins of Mycobacterium tuberculosis." Song H., Sandie R., Wang Y., Andrade-Navarro M.A., Niederweis M. Tuberculosis 88:526-544(2008) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION. Strain: ATCC 25618 / H37Rv.
[6]	"Expression of the ompATb operon accelerates ammonia secretion and adaptation of Mycobacterium tuberculosis to acidic environments." Song H., Huff J., Janik K., Walter K., Keller C., Ehlers S., Bossmann S.H., Niederweis M. Mol. Microbiol. 80:900-918(2011) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN AMMONIA SECRETION, INDUCTION, DISRUPTION PHENOTYPE. Strain: ATCC 25618 / H37Rv.
[7]	"Mycobacterium tuberculosis Rv0899 adopts a mixed alpha/beta-structure and does not form a transmembrane beta-barrel." Teriete P., Yao Y., Kolodzik A., Yu J., Song H., Niederweis M., Marassi F.M. Biochemistry 49:2768-2777(2010) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 73-203, SUBUNIT.
[8]	"Structural studies of Mycobacterium tuberculosis Rv0899 reveal a monomeric membrane-anchoring protein with two separate domains." Li J., Shi C., Gao Y., Wu K., Shi P., Lai C., Chen L., Wu F., Tian C. J. Mol. Biol. 415:382-392(2012) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 52-326, SUBUNIT, DISULFIDE BOND, PUTATIVE ZINC-BINDING.
[9]	"Molecular structure and peptidoglycan recognition of Mycobacterium tuberculosis ArfA (Rv0899)." Yao Y., Barghava N., Kim J., Niederweis M., Marassi F.M. J. Mol. Biol. 416:208-220(2012) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 196-326, DISULFIDE BOND, PEPTIDOGLYCAN-BINDING, MUTAGENESIS OF LEU-232; ASP-236 AND ARG-277. Strain: ATCC 25618 / H37Rv.
[10]	"Structure of the Mycobacterium tuberculosis OmpATb protein: a model of an oligomeric channel in the mycobacterial cell wall." Yang Y., Auguin D., Delbecq S., Dumas E., Molle G., Molle V., Roumestand C., Saint N. Proteins 79:645-661(2011) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 73-204 AND OF 198-326, DISULFIDE BOND, SUBUNIT. Strain: ATCC 25618 / H37Rv.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BX842574 Genomic DNA. Translation: CAA97374.1.
AE000516 Genomic DNA. Translation: AAK45169.1.
AL123456 Genomic DNA. Translation: CCP43647.1.

PIR

H70782.

RefSeq

NP_215414.1. NC_000962.3.
NP_335355.1. NC_002755.2.
YP_006514252.1. NC_018143.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2KGS	NMR	-	A	73-204	[»]
2KGW	NMR	-	A	198-326	[»]
2KSM	NMR	-	A	73-203	[»]
2L26	NMR	-	A	52-326	[»]
2LBT	NMR	-	A	196-326	[»]
2LCA	NMR	-	A	196-326	[»]

ProteinModelPortal

P65593.

SMR

P65593. Positions 88-326.

ModBase

Search...

Protein-protein interaction databases

STRING

83332.Rv0899.

Protein family/group databases

TCDB

1.B.6.1.3. OmpA-OmpF porin (OOP) family.

Proteomic databases

PRIDE

P65593.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAK45169; AAK45169; MT0922.

GeneID

13318803.
885286.
926237.

KEGG

mtc:MT0922.
mtu:Rv0899.
mtv:RVBD_0899.

PATRIC

18123776. VBIMycTub22151_1012.

Organism-specific databases

TubercuList

Rv0899.

Phylogenomic databases

eggNOG

COG2885.

HOGENOM

HOG000042132.

KO

K16191.

OMA

TDHITAK.

ProtClustDB

CLSK790818.

Family and domain databases

Gene3D

3.30.1330.60. 1 hit.

InterPro

IPR007055. BON_dom.
IPR006664. OMP_bac.
IPR006690. OMPA-like_CS.
IPR006665. OmpA/MotB_C.
[Graphical view]

Pfam

PF04972. BON. 2 hits.
PF00691. OmpA. 1 hit.
[Graphical view]

PRINTS

PR01021. OMPADOMAIN.

SUPFAM

SSF103088. OmpA/MotB_C. 1 hit.

PROSITE

PS50914. BON. False negative.
PS01068. OMPA_1. 1 hit.
PS51123. OMPA_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P65593.

Entry information

Entry name

ARFA_MYCTU

Accession

Primary (citable) accession number: P65593
Secondary accession number(s): L0T818, Q10557

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2004
Last sequence update:	October 11, 2004
Last modified:	May 1, 2013
This is version 72 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program