{"entryType":"UniProtKB reviewed (Swiss-Prot)","primaryAccession":"A4ZFB2","uniProtkbId":"SCAF_BP80A","entryAudit":{"firstPublicDate":"2024-03-27","lastAnnotationUpdateDate":"2026-09-02","lastSequenceUpdateDate":"2007-05-29","entryVersion":49,"sequenceVersion":1},"annotationScore":5.0,"organism":{"scientificName":"Staphylococcus phage 80alpha","taxonId":53369,"lineage":["Viruses","Duplodnaviria","Heunggongvirae","Uroviricota","Caudoviricetes","Caudoviricetes incertae sedis","Azeredovirinae","Dubowvirus"]},"organismHosts":[{"scientificName":"Staphylococcus aureus","taxonId":1280}],"proteinExistence":"1: Evidence at protein level","proteinDescription":{"recommendedName":{"fullName":{"evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"17693489"},{"evidenceCode":"ECO:0000303","source":"PubMed","id":"20869739"}],"value":"Capsid assembly scaffolding protein"},"shortNames":[{"evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"28984245"}],"value":"SP"}]},"alternativeNames":[{"fullName":{"evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"37968393"}],"value":"Gp46 protein"}}],"flag":"Precursor"},"genes":[{"geneName":{"evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"18565341"}],"value":"gp46"}}],"comments":[{"texts":[{"evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"P13848"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28984245"}],"value":"Scaffolding protein involved in icosahedric procapsid assembly. Coassembles with capsid protein(s) to form the procapsid (PubMed:28984245). The scaffolding protein is found within the capsid as a series of concentric shells. During DNA packaging, the scaffolding protein molecules are released from the procapsid (By similarity)"}],"commentType":"FUNCTION"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28984245"}],"value":"Found in the procapsid with the major capsid protein in a 2:1 capsid protein:scaffold protein molecular ratio (PubMed:28984245)"}],"commentType":"SUBUNIT"},{"commentType":"SUBCELLULAR LOCATION","note":{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"17693489"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"18565341"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28984245"}],"value":"Found in provirions but not in mature virions"}]}},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28984245"}],"value":"In the 80alpha procapsid the C-terminal 21 residues of SP form a helix-and-hook motif that interacts extensively with the major capsid protein, especially with the N-arm (approximately residues 26-70 in the capsid protein) (PubMed:28984245)"}],"commentType":"DOMAIN"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"25388641"}],"value":"The N-terminus is cleaved by ribosomal processing protease Prp (PubMed:25388641)"}],"commentType":"PTM"},{"commentType":"MASS SPECTROMETRY","method":"Electrospray","molWeight":21700.5,"molWeightError":0.07,"note":"Mature form, residues 14-206.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"18565341"}]},{"commentType":"MASS SPECTROMETRY","method":"MALDI","molWeight":21701.0,"molWeightError":0.0,"note":"Mature form processed by Prp.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"25388641"}]},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"37968393"}],"value":"When the gene is mutated the virus becomes resistant to the host CBASS CdnE-Cap15 system without altering the production of 3',2'-cGAMP or cabRNA by host CdnE; the host Cap15 effector protein seems to be activated but the virus still completes its replication cycle (PubMed:37968393)"}],"commentType":"MISCELLANEOUS"}],"features":[{"type":"Propeptide","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":13,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"18565341"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"25388641"}],"featureId":"PRO_0000459834"},{"type":"Chain","location":{"start":{"value":14,"modifier":"EXACT"},"end":{"value":206,"modifier":"EXACT"}},"description":"Capsid assembly scaffolding protein","featureId":"PRO_0000459835"},{"type":"Region","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":50,"modifier":"EXACT"}},"description":"Disordered","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Region","location":{"start":{"value":83,"modifier":"EXACT"},"end":{"value":134,"modifier":"EXACT"}},"description":"Disordered","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Region","location":{"start":{"value":173,"modifier":"EXACT"},"end":{"value":206,"modifier":"EXACT"}},"description":"Disordered","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Region","location":{"start":{"value":186,"modifier":"EXACT"},"end":{"value":206,"modifier":"EXACT"}},"description":"Helix-and-hook motif","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28984245"}]},{"type":"Compositional bias","location":{"start":{"value":25,"modifier":"EXACT"},"end":{"value":38,"modifier":"EXACT"}},"description":"Basic and acidic residues","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Compositional bias","location":{"start":{"value":83,"modifier":"EXACT"},"end":{"value":127,"modifier":"EXACT"}},"description":"Basic and acidic residues","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Compositional bias","location":{"start":{"value":173,"modifier":"EXACT"},"end":{"value":192,"modifier":"EXACT"}},"description":"Polar residues","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Mutagenesis","location":{"start":{"value":2,"modifier":"EXACT"},"end":{"value":13,"modifier":"EXACT"}},"description":"No viable phage, greatly reduced levels of capsid protein, accumulates large numbers of tails.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"29258203"}],"alternativeSequence":{"originalSequence":"EENKLKFNLQFF","alternativeSequences":["AA"]}},{"type":"Mutagenesis","location":{"start":{"value":2,"modifier":"EXACT"},"end":{"value":13,"modifier":"EXACT"}},"description":"Wild-type phage titer and viability.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"29258203"}],"alternativeSequence":{}},{"type":"Mutagenesis","location":{"start":{"value":105,"modifier":"EXACT"},"end":{"value":105,"modifier":"EXACT"}},"description":"Virus escapes the CBASS system in host bacteria, allowing virus propagation. Phage still activates 3',2'-cGAMP production and makes wild-type cabRNA.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"37968393"}],"alternativeSequence":{"originalSequence":"E","alternativeSequences":["D"]}},{"type":"Mutagenesis","location":{"start":{"value":186,"modifier":"EXACT"},"end":{"value":206,"modifier":"EXACT"}},"description":"Slightly reduced phage titer.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28984245"}],"alternativeSequence":{"originalSequence":"STKNKPQNLAEIARQKRIIKN","alternativeSequences":["KQKQYGTTLQNLAKQNRIIK"]}},{"type":"Mutagenesis","location":{"start":{"value":198,"modifier":"EXACT"},"end":{"value":198,"modifier":"EXACT"}},"description":"Defective in producing infectious virions.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28984245"}],"alternativeSequence":{"originalSequence":"A","alternativeSequences":["I"]}},{"type":"Mutagenesis","location":{"start":{"value":202,"modifier":"EXACT"},"end":{"value":202,"modifier":"EXACT"}},"description":"Defective in producing infectious virions.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28984245"}],"alternativeSequence":{"originalSequence":"R","alternativeSequences":["E","K","S"]}},{"type":"Mutagenesis","location":{"start":{"value":203,"modifier":"EXACT"},"end":{"value":203,"modifier":"EXACT"}},"description":"Defective in producing infectious virions.","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28984245"}],"alternativeSequence":{"originalSequence":"I","alternativeSequences":["T"]}}],"keywords":[{"id":"KW-0002","category":"Technical term","name":"3D-structure"},{"id":"KW-0903","category":"Technical term","name":"Direct protein sequencing"},{"id":"KW-0945","category":"Biological process","name":"Host-virus interaction"},{"id":"KW-1090","category":"Biological process","name":"Inhibition of host innate immune response by virus"},{"id":"KW-0426","category":"Developmental stage","name":"Late protein"},{"id":"KW-1185","category":"Technical term","name":"Reference proteome"},{"id":"KW-0118","category":"Biological process","name":"Viral capsid assembly"},{"id":"KW-0899","category":"Biological process","name":"Viral immunoevasion"},{"id":"KW-1188","category":"Biological process","name":"Viral release from host cell"}],"references":[{"referenceNumber":1,"citation":{"id":"17693489","citationType":"journal article","authors":["Tallent S.M.","Langston T.B.","Moran R.G.","Christie G.E."],"citationCrossReferences":[{"database":"PubMed","id":"17693489"},{"database":"DOI","id":"10.1128/jb.00738-07"}],"title":"Transducing particles of Staphylococcus aureus pathogenicity island SaPI1 are comprised of helper phage-encoded proteins.","publicationDate":"2007","journal":"J. Bacteriol.","firstPage":"7520","lastPage":"7524","volume":"189"},"referencePositions":["NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]","PROTEIN SEQUENCE OF 36-59; 124-162 AND 174-199","SUBCELLULAR LOCATION"],"evidences":[{"evidenceCode":"ECO:0000312","source":"EMBL","id":"ABF71617.1"}]},{"referenceNumber":2,"citation":{"id":"20869739","citationType":"journal article","authors":["Christie G.E.","Matthews A.M.","King D.G.","Lane K.D.","Olivarez N.P.","Tallent S.M.","Gill S.R.","Novick R.P."],"citationCrossReferences":[{"database":"PubMed","id":"20869739"},{"database":"DOI","id":"10.1016/j.virol.2010.08.036"}],"title":"The complete genomes of Staphylococcus aureus bacteriophages 80 and 80alpha--implications for the specificity of SaPI mobilization.","publicationDate":"2010","journal":"Virology","firstPage":"381","lastPage":"390","volume":"407"},"referencePositions":["NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]"],"evidences":[{"evidenceCode":"ECO:0000312","source":"EMBL","id":"ABF71617.1"}]},{"referenceNumber":3,"citation":{"id":"18565341","citationType":"journal article","authors":["Poliakov A.","Chang J.R.","Spilman M.S.","Damle P.K.","Christie G.E.","Mobley J.A.","Dokland T."],"citationCrossReferences":[{"database":"PubMed","id":"18565341"},{"database":"DOI","id":"10.1016/j.jmb.2008.04.065"}],"title":"Capsid size determination by Staphylococcus aureus pathogenicity island SaPI1 involves specific incorporation of SaPI1 proteins into procapsids.","publicationDate":"2008","journal":"J. Mol. Biol.","firstPage":"465","lastPage":"475","volume":"380"},"referencePositions":["SUBCELLULAR LOCATION","MASS SPECTROMETRY"]},{"referenceNumber":4,"citation":{"id":"25388641","citationType":"journal article","authors":["Wall E.A.","Caufield J.H.","Lyons C.E.","Manning K.A.","Dokland T.","Christie G.E."],"citationCrossReferences":[{"database":"PubMed","id":"25388641"},{"database":"DOI","id":"10.1111/mmi.12862"}],"title":"Specific N-terminal cleavage of ribosomal protein L27 in Staphylococcus aureus and related bacteria.","publicationDate":"2015","journal":"Mol. Microbiol.","firstPage":"258","lastPage":"269","volume":"95"},"referencePositions":["PROTEOLYTIC CLEAVAGE","MASS SPECTROMETRY"]},{"referenceNumber":5,"citation":{"id":"29258203","citationType":"journal article","authors":["Kizziah J.L.","Manning K.A.","Dearborn A.D.","Wall E.A.","Klenow L.","Hill R.L.L.","Spilman M.S.","Stagg S.M.","Christie G.E.","Dokland T."],"citationCrossReferences":[{"database":"PubMed","id":"29258203"},{"database":"DOI","id":"10.3390/v9120384"}],"title":"Cleavage and Structural Transitions during Maturation of Staphylococcus aureus Bacteriophage 80alpha and SaPI1 Capsids.","publicationDate":"2017","journal":"Viruses","firstPage":"0","lastPage":"0","volume":"9"},"referencePositions":["MUTAGENESIS OF 2-GLU--PHE-13"]},{"referenceNumber":6,"citation":{"id":"37968393","citationType":"journal article","authors":["Banh D.V.","Roberts C.G.","Morales-Amador A.","Berryhill B.A.","Chaudhry W.","Levin B.R.","Brady S.F.","Marraffini L.A."],"citationCrossReferences":[{"database":"PubMed","id":"37968393"},{"database":"DOI","id":"10.1038/s41586-023-06743-9"}],"title":"Bacterial cGAS senses a viral RNA to initiate immunity.","publicationDate":"2023","journal":"Nature","firstPage":"0","lastPage":"0","volume":"0"},"referencePositions":["CBASS RESISTANCE","MUTAGENESIS OF GLU-105"]},{"referenceNumber":7,"citation":{"id":"28984245","citationType":"journal article","authors":["Dearborn A.D.","Wall E.A.","Kizziah J.L.","Klenow L.","Parker L.K.","Manning K.A.","Spilman M.S.","Spear J.M.","Christie G.E.","Dokland T."],"citationCrossReferences":[{"database":"PubMed","id":"28984245"},{"database":"DOI","id":"10.7554/elife.30822"}],"title":"Competing scaffolding proteins determine capsid size during mobilization of Staphylococcus aureus pathogenicity islands.","publicationDate":"2017","journal":"Elife","firstPage":"e30822","lastPage":"e30822","volume":"6"},"referencePositions":["STRUCTURE BY ELECTRON MICROSCOPY (3.72 ANGSTROMS) OF 191-206","FUNCTION","SUBUNIT","SUBCELLULAR LOCATION","DOMAIN","MUTAGENESIS OF 186-SER--ASN-206; ALA-198; ARG-202 AND ILE-203"],"evidences":[{"evidenceCode":"ECO:0007744","source":"PDB","id":"6B0X"}]}],"uniProtKBCrossReferences":[{"database":"EMBL","id":"DQ517338","properties":[{"key":"ProteinId","value":"ABF71617.1"},{"key":"Status","value":"-"},{"key":"MoleculeType","value":"Genomic_DNA"}]},{"database":"RefSeq","id":"YP_001285360.1","properties":[{"key":"NucleotideSequenceId","value":"NC_009526.1"}]},{"database":"PDB","id":"6B0X","properties":[{"key":"Method","value":"EM"},{"key":"Resolution","value":"3.80 A"},{"key":"Chains","value":"a/b/c/d/e/f/g=1-206"}]},{"database":"PDBsum","id":"6B0X","properties":[{"key":"Description","value":"-"}]},{"database":"EMDB","id":"EMD-7030","properties":[{"key":"Description","value":"-"}]},{"database":"SMR","id":"A4ZFB2","properties":[{"key":"Description","value":"-"}]},{"database":"GeneID","id":"5246935","properties":[{"key":"Description","value":"-"}]},{"database":"KEGG","id":"vg:5246935","properties":[{"key":"Description","value":"-"}]},{"database":"OrthoDB","id":"14655at10239","properties":[{"key":"Description","value":"-"}]},{"database":"Proteomes","id":"UP000201164","properties":[{"key":"Component","value":"Segment"}]},{"database":"GO","id":"GO:0046806","properties":[{"key":"GoTerm","value":"C:viral scaffold"},{"key":"GoEvidenceType","value":"IMP:CACAO"}],"evidences":[{"evidenceCode":"ECO:0000315","source":"PubMed","id":"22980502"}]},{"database":"GO","id":"GO:0052170","properties":[{"key":"GoTerm","value":"P:symbiont-mediated suppression of host innate immune response"},{"key":"GoEvidenceType","value":"IEA:UniProtKB-KW"}]},{"database":"InterPro","id":"IPR025580","properties":[{"key":"EntryName","value":"Gp46"}]},{"database":"Pfam","id":"PF14265","properties":[{"key":"EntryName","value":"DUF4355"},{"key":"MatchStatus","value":"1"}]}],"sequence":{"value":"MEENKLKFNLQFFADQSDDPDEPGGDGKKGNPDKKENDEGTEITFTPEQQKKVDEILERRVAHEKKKADEYAKEKAAEAAKEAAKLAKMNKDQKDEYEREQMEKELEQLRSEKQLNEMRSEARKMLSEAEVDSSDEVVNLVVTDTAEQTKSNVEAFSNAVKKAVNEAVKVNARQSPLTGGDSFNHSTKNKPQNLAEIARQKRIIKN","length":206,"molWeight":23371,"crc64":"9B12C592984ACCAE","md5":"458879FAE470C680CFCB5572C5A18F23"},"extraAttributes":{"countByCommentType":{"FUNCTION":1,"SUBUNIT":1,"SUBCELLULAR LOCATION":1,"DOMAIN":1,"PTM":1,"MASS SPECTROMETRY":2,"MISCELLANEOUS":1},"countByFeatureType":{"Propeptide":1,"Chain":1,"Region":4,"Compositional bias":3,"Mutagenesis":7},"uniParcId":"UPI000050586A"}}