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UniProtKB - P9WIU5 (ARFA_MYCTU)

Entry version 33 (02 Dec 2020)
Sequence version 1 (16 Apr 2014)
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Protein

Peptidoglycan-binding protein ArfA

Gene

arfA

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

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.3 Publications

Caution

Was originally thought to be a porin.1 Publication

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Zn2+Note: May bind Zn2+ via residues in the BON domain.

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Biological processIon transport, Transport
LigandMetal-binding, Zinc

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Peptidoglycan-binding protein ArfA
Alternative name(s):
Outer membrane porin A
Outer membrane protein A
Short name:
OmpATb
Outer membrane protein ArfA
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:arfA
Synonyms:ompA
Ordered Locus Names:Rv0899
ORF Names:MTCY31.27
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83332 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Actinobacteria › Corynebacteriales › Mycobacteriaceae › Mycobacterium › Mycobacterium tuberculosis complex ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000001584 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

Organism-specific databases

Mycobacterium tuberculosis strain H37Rv genome database

More...TubercuListi		Rv0899

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/subcellular%5Flocation%5Fsection">'Subcellular location'</a> section describes the extent of a membrane-spanning region of the protein. It denotes the presence of both alpha-helical transmembrane regions and the membrane spanning regions of beta-barrel transmembrane proteins.<p><a href='/help/transmem' target='_top'>More...</a></p>Transmembranei30 – 50HelicalSequence analysisAdd BLAST21

GO - Cellular componenti

Complete GO annotation on QuickGO ...

Keywords - Cellular componenti

Cell outer membrane, Cell wall, Membrane, Secreted

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

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 (PubMed:12366842). But the same mutant has very little effect when studied by another group (PubMed:21410778). 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 (PubMed:21410778).2 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi232L → G: Decreases structure stability of OmpA-like domain. 1 Publication1
Mutagenesisi236D → A: Increases conformational stability of OmpA-like domain. Does not alter peptidoglycan-binding. 1 Publication1
Mutagenesisi277R → E: Loss of peptidoglycan-binding; in association with A236. 1 Publication1

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001962591 – 326Peptidoglycan-binding protein ArfAAdd BLAST326

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the PTM / Processing":/help/ptm_processing_section section describes the positions of cysteine residues participating in disulfide bonds.<p><a href='/help/disulfid' target='_top'>More...</a></p>Disulfide bondi208 ↔ 2503 Publications

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P9WIU5

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

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.2 Publications

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Controversial; may form oligomers (PubMed:17573469, PubMed:21117233), or not (PubMed:20199110, PubMed:21117233).

4 Publications

Protein-protein interaction databases

STRING: functional protein association networks

More...STRINGi		83332.Rv0899

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1326
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Biological Magnetic Resonance Data Bank

More...BMRBi		P9WIU5

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P9WIU5

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family%5Fand%5Fdomains%5Fsection">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini127 – 196BONAdd BLAST70
Domaini212 – 326OmpA-likePROSITE-ProRule annotationAdd BLAST115

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 73Required for protein translocation to the outer membraneAdd BLAST73

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the outer membrane OOP (TC 1.B.6) superfamily. ArfA family. [View classification]Curated

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG2885, Bacteria

Identification of Orthologs from Complete Genome Data

More...OMAi		MKGEVHN

Family and domain databases

Conserved Domains Database

More...CDDi		cd07185, OmpA_C-like, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.30.1330.60, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR007055, BON_dom
IPR006664, OMP_bac
IPR006665, OmpA-like
IPR006690, OMPA-like_CS
IPR036737, OmpA-like_sf

Pfam protein domain database

More...Pfami		View protein in Pfam
PF04972, BON, 1 hit
PF00691, OmpA, 1 hit

Protein Motif fingerprint database; a protein domain database

More...PRINTSi		PR01021, OMPADOMAIN

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF103088, SSF103088, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS01068, OMPA_1, 1 hit
PS51123, OMPA_2, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P9WIU5-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MASKAGLGQT PATTDARRTQ KFYRGSPGRP WLIGAVVIPL LIAAIGYGAF 
        60         70         80         90        100
ERPQSVTGPT GVLPTLTPTS TRGASALSLS LLSISRSGNT VTLIGDFPDE 
       110        120        130        140        150
AAKAALMTAL NGLLAPGVNV IDQIHVDPVV RSLDFSSAEP VFTASVPIPD 
       160        170        180        190        200
FGLKVERDTV TLTGTAPSSE HKDAVKRAAT STWPDMKIVN NIEVTGQAPP 
       210        220        230        240        250
GPPASGPCAD LQSAINAVTG GPIAFGNDGA SLIPADYEIL NRVADKLKAC 
       260        270        280        290        300
PDARVTINGY TDNTGSEGIN IPLSAQRAKI VADYLVARGV AGDHIATVGL 
       310        320 
GSVNPIASNA TPEGRAKNRR VEIVVN
Length:326
Mass (Da):33,574
Last modified:April 16, 2014 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i9E0D46ABCC179F4A
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
AL123456 Genomic DNA Translation: CCP43647.1

Protein sequence database of the Protein Information Resource

More...PIRi		H70782

NCBI Reference Sequences

More...RefSeqi		NP_215414.1, NC_000962.3
WP_003404684.1, NZ_NVQJ01000001.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		CCP43647; CCP43647; Rv0899

Database of genes from NCBI RefSeq genomes

More...GeneIDi		23492977
885286

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		mtu:Rv0899
mtv:RVBD_0899

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL123456 Genomic DNA Translation: CCP43647.1
PIRiH70782
RefSeqiNP_215414.1, NC_000962.3
WP_003404684.1, NZ_NVQJ01000001.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...PDBei

Protein Data Bank RCSB

More...RCSB PDBi

Protein Data Bank Japan

More...PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KGSNMR-A73-204[»]
2KGWNMR-A198-326[»]
2KSMNMR-A73-203[»]
2L26NMR-A52-326[»]
2LBTNMR-A196-326[»]
2LCANMR-A196-326[»]
BMRBiP9WIU5
SMRiP9WIU5
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi83332.Rv0899

Proteomic databases

PaxDbiP9WIU5

Genome annotation databases

EnsemblBacteriaiCCP43647; CCP43647; Rv0899
GeneIDi23492977
885286
KEGGimtu:Rv0899
mtv:RVBD_0899

Organism-specific databases

TubercuListiRv0899

Phylogenomic databases

eggNOGiCOG2885, Bacteria
OMAiMKGEVHN

Family and domain databases

CDDicd07185, OmpA_C-like, 1 hit
Gene3Di3.30.1330.60, 1 hit
InterProiView protein in InterPro
IPR007055, BON_dom
IPR006664, OMP_bac
IPR006665, OmpA-like
IPR006690, OMPA-like_CS
IPR036737, OmpA-like_sf
PfamiView protein in Pfam
PF04972, BON, 1 hit
PF00691, OmpA, 1 hit
PRINTSiPR01021, OMPADOMAIN
SUPFAMiSSF103088, SSF103088, 1 hit
PROSITEiView protein in PROSITE
PS01068, OMPA_1, 1 hit
PS51123, OMPA_2, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...ProtoNeti		Search...

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiARFA_MYCTU
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P9WIU5
Secondary accession number(s): L0T818, P65593, Q10557
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 16, 2014
Last sequence update: April 16, 2014
Last modified: December 2, 2020
This is version 33 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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