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Protein

Superoxide dismutase-like protein YojM

Gene

yojM

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Cofactori

Zn2+Note: Binds 1 zinc ion per homodimer. The zinc ion is bound between 2 subunits and mediates dimerization.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi71 – 711Zinc; shared with dimeric partner; structural
Metal bindingi86 – 861CopperSequence Analysis
Metal bindingi137 – 1371Zinc; shared with dimeric partner; structural
Metal bindingi166 – 1661CopperSequence Analysis

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Ligandi

Copper, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciBSUB:BSU19400-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Superoxide dismutase-like protein YojM
Gene namesi
Name:yojM
Ordered Locus Names:BSU19400
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570 Componenti: Chromosome

Organism-specific databases

GenoListiBSU19400.

Subcellular locationi

  • Cell membrane PROSITE-ProRule annotation; Lipid-anchor PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi88 – 881Y → H: Leads to copper binding and enzyme activity; when associated with H-104. 1 Publication
Mutagenesisi104 – 1041P → H: Leads to copper binding and enzyme activity; when associated with H-88. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1717PROSITE-ProRule annotationAdd
BLAST
Chaini18 – 196179Superoxide dismutase-like protein YojMPRO_0000032842Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Lipidationi18 – 181N-palmitoyl cysteinePROSITE-ProRule annotation
Lipidationi18 – 181S-diacylglycerol cysteinePROSITE-ProRule annotation
Disulfide bondi93 ↔ 186

Keywords - PTMi

Disulfide bond, Lipoprotein, Palmitate

Proteomic databases

PaxDbiO31851.

Interactioni

Subunit structurei

Monomer, and homodimer. Largely unstructured monomer in solution. Well-ordered homodimer in the crystal.2 Publications

Protein-protein interaction databases

IntActiO31851. 19 interactions.
STRINGi224308.Bsubs1_010100010711.

Structurei

Secondary structure

1
196
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi42 – 498Combined sources
Turni50 – 523Combined sources
Beta strandi54 – 629Combined sources
Beta strandi64 – 7411Combined sources
Beta strandi85 – 906Combined sources
Turni91 – 933Combined sources
Turni95 – 973Combined sources
Helixi99 – 1013Combined sources
Beta strandi124 – 1296Combined sources
Beta strandi136 – 1427Combined sources
Beta strandi149 – 1524Combined sources
Beta strandi154 – 1574Combined sources
Beta strandi161 – 1688Combined sources
Beta strandi172 – 1743Combined sources
Turni175 – 1795Combined sources
Beta strandi182 – 1898Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1S4IX-ray1.80A/B/C/D22-196[»]
1U3NNMR-A35-196[»]
1XTLX-ray2.00A/B/C/D22-196[»]
1XTMX-ray1.60A/B22-196[»]
DisProtiDP00257.
ProteinModelPortaliO31851.
SMRiO31851. Positions 40-191.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO31851.

Family & Domainsi

Sequence similaritiesi

Belongs to the Cu-Zn superoxide dismutase family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiCOG2032.
HOGENOMiHOG000263448.
InParanoidiO31851.
KOiK04565.
OMAiAPRFESS.
OrthoDBiEOG6K13RS.
PhylomeDBiO31851.

Family and domain databases

Gene3Di2.60.40.200. 1 hit.
InterProiIPR001424. SOD_Cu_Zn_dom.
[Graphical view]
PfamiPF00080. Sod_Cu. 1 hit.
[Graphical view]
SUPFAMiSSF49329. SSF49329. 1 hit.
PROSITEiPS51257. PROKAR_LIPOPROTEIN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O31851-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHRLLLLMML TALGVAGCGQ KKPPDPPNRV PEKKVVETSA FGHHVQLVNR
60 70 80 90 100
EGKAVGFIEI KESDDEGLDI HISANSLRPG ASLGFHIYEK GSCVRPDFES
110 120 130 140 150
AGGPFNPLNK EHGFNNPMGH HAGDLPNLEV GADGKVDVIM NAPDTSLKKG
160 170 180 190
SKLNILDEDG SAFIIHEQAD DYLTNPSGNS GARIVCGALL GNNEKQ
Length:196
Mass (Da):20,953
Last modified:January 1, 1998 - v1
Checksum:i7C00301A62188306
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF026147 Genomic DNA. Translation: AAC17861.1.
AL009126 Genomic DNA. Translation: CAB13832.1.
PIRiB69907.
RefSeqiNP_389822.1. NC_000964.3.
WP_004399243.1. NZ_JNCM01000036.1.

Genome annotation databases

EnsemblBacteriaiCAB13832; CAB13832; BSU19400.
GeneIDi939502.
KEGGibsu:BSU19400.
PATRICi18975731. VBIBacSub10457_2056.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF026147 Genomic DNA. Translation: AAC17861.1.
AL009126 Genomic DNA. Translation: CAB13832.1.
PIRiB69907.
RefSeqiNP_389822.1. NC_000964.3.
WP_004399243.1. NZ_JNCM01000036.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1S4IX-ray1.80A/B/C/D22-196[»]
1U3NNMR-A35-196[»]
1XTLX-ray2.00A/B/C/D22-196[»]
1XTMX-ray1.60A/B22-196[»]
DisProtiDP00257.
ProteinModelPortaliO31851.
SMRiO31851. Positions 40-191.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiO31851. 19 interactions.
STRINGi224308.Bsubs1_010100010711.

Proteomic databases

PaxDbiO31851.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13832; CAB13832; BSU19400.
GeneIDi939502.
KEGGibsu:BSU19400.
PATRICi18975731. VBIBacSub10457_2056.

Organism-specific databases

GenoListiBSU19400.

Phylogenomic databases

eggNOGiCOG2032.
HOGENOMiHOG000263448.
InParanoidiO31851.
KOiK04565.
OMAiAPRFESS.
OrthoDBiEOG6K13RS.
PhylomeDBiO31851.

Enzyme and pathway databases

BioCyciBSUB:BSU19400-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO31851.

Family and domain databases

Gene3Di2.60.40.200. 1 hit.
InterProiIPR001424. SOD_Cu_Zn_dom.
[Graphical view]
PfamiPF00080. Sod_Cu. 1 hit.
[Graphical view]
SUPFAMiSSF49329. SSF49329. 1 hit.
PROSITEiPS51257. PROKAR_LIPOPROTEIN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sequence analysis of the Bacillus subtilis 168 chromosome region between the sspC and odhA loci (184 degrees-180 degrees)."
    Ghim S.-Y., Choi S.-K., Shin B.-S., Jeong Y.-M., Sorokin A., Ehrlich S.D., Park S.-H.
    DNA Res. 5:195-201(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.
  3. "From an inactive prokaryotic SOD homologue to an active protein through site-directed mutagenesis."
    Banci L., Benvenuti M., Bertini I., Cabelli D.E., Calderone V., Fantoni A., Mangani S., Migliardi M., Viezzoli M.S.
    J. Am. Chem. Soc. 127:13287-13292(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 22-196 OF MUTANT HIS-88/HIS-104 IN COMPLEX WITH COPPER AND ZINC IONS, MUTAGENESIS OF TYR-88 AND PRO-104.
  4. "A prokaryotic superoxide dismutase paralog lacking two Cu ligands: from largely unstructured in solution to ordered in the crystal."
    Banci L., Bertini I., Calderone V., Cramaro F., Del Conte R., Fantoni A., Mangani S., Quattrone A., Viezzoli M.S.
    Proc. Natl. Acad. Sci. U.S.A. 102:7541-7546(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 22-196 IN COMPLEX WITH ZINC IONS, SUBUNIT.

Entry informationi

Entry nameiYOJM_BACSU
AccessioniPrimary (citable) accession number: O31851
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 11, 2001
Last sequence update: January 1, 1998
Last modified: June 24, 2015
This is version 120 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.