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Entry version 69 (07 Apr 2021)
Sequence version 1 (06 Dec 2005)
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Protein

Carboxysome shell protein CcmK4

Gene

ccmK4

Organism
Synechococcus elongatus (strain PCC 7942 / FACHB-805) (Anacystis nidulans R2)
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

One of the shell proteins of the carboxysome, a polyhedral inclusion where RuBisCO (ribulose bisphosphate carboxylase, rbcL-rbcS) is sequestered. Assembles into hexamers which make sheets that form the facets of the polyhedral carboxysome. The hexamer central pore probably regulates metabolite flux.UniRule annotation
A minor shell protein of the carboxysome, a polyhedral inclusion where RuBisCO (ribulose bisphosphate carboxylase, rbcL-rbcS) is sequestered (Probable). Hexamers form sheets that form the facets of the polyhedral carboxysome. The shell is 4.5 nm thick, as observed for CcmK proteins (PubMed:28616951). In PCC 7942 there are several CcmK paralogs with presumably functional differences; replacing the central pore residues (34-37) with those of CcmK2 from this organism (Tyr-Glu-Lys-Ile) allows the bacterium to make carboxysomes, but the expression level is too low to know if the carboxysome is functional for CO2 fixation (Probable). This subunit probably makes both homohexamers and heterohexamers with CcmK3. The CcmK3-CcmK4 heterohexmers have been suggested to cap other hexamers, perhaps to alter metabolite flux (Probable).3 Publications1 Publication

<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

GO - Biological processi

<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 processCarbon dioxide fixation, Photosynthesis

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
SYNEL:SYNPCC7942_0285-MONOMER

<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:
Carboxysome shell protein CcmK41 Publication
Alternative name(s):
Carbon dioxide-concentrating mechanism protein CcmK4
<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:ccmK41 Publication
Ordered Locus Names:Synpcc7942_0285
<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>OrganismiSynechococcus elongatus (strain PCC 7942 / FACHB-805) (Anacystis nidulans R2)
<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 identifieri1140 [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 lineageiBacteriaCyanobacteriaSynechococcalesSynechococcaceaeSynechococcus
<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
  • UP000002717 <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

<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

Keywords - Cellular componenti

Carboxysome

<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 use of a specific protein in the biotechnological industry.<p><a href='/help/biotechnological_use' target='_top'>More...</a></p>Biotechnological usei

Heterologous expression of 12 carboxysomal genes in E.coli (ccaA, ccmK2, ccmK3, ccmK4, ccmL, ccmM, ccmN, ccmO, ccmP, rbcL, rbcS, rbcX) leads to the formation of bodies that resemble carboxysomes, have densely packed paracrystalline arrays and RuBisCO activity. These structures open the door to generating carboxysomes in plant cells to increase their photosynthesis and productivity, as well as tailoring bacterial microcompartments to specific metabolic needs and molecule delivery. The absence of ccaA, ccmK3, ccmK4, ccmP and rbcX leads to less active RuBisCO.1 Publication

<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

Single deletion has a wild-type phenotype, a double ccmK3-ccmK4 deletion has slightly larger, aggregated instead of spatially separated carboxysomes, and has a photosynthetic affinity for inorganic carbon between wild-type and carboxysome-less strains (PubMed:22928045). In another study single mutant grows slower in air and low light, double ccmK3-ccmK4 mutant has similarly impaired growth rate; ccmK3 does not complement the double deletion, while ccmK4 does (PubMed:30389783).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>Mutagenesisi36 – 38MRA → EKI: Probably alters pore properties, is able to form carboxysomes, residues correspond to CcmK2 of this organism. 1 Publication3
Mutagenesisi40S → D: Does not complement its deletion mutant, forms homohexamers in vitro. 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_00004512361 – 113Carboxysome shell protein CcmK4Add BLAST113

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
Q31RK2

<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

Carboxysome size and components vary with growth conditions. When grown in ambient air at medium light (50 uE meter(-2) second(-1)) there are 52 units of this protein per carboxysome, the numbers are stable under low light and high light, and increase under high CO2 (at protein level). The CcmK3:CcmK4 ratio of 1:3.8 is stable over all growth conditions.1 Publication

<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

Homohexamer (PubMed:25117559).

Interacts stably with CcmK3, probably forms heterohexamers with a 1:2 CcmK3:CcmK4 stoichiometry (PubMed:30389783) (Probable).

1 Publication2 Publications

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
1140.Synpcc7942_0285

<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

1113
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

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SMRi
Q31RK2

Database of comparative protein structure models

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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>Domaini5 – 91BMCUniRule annotationAdd BLAST87

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The tight homohexamer forms a pore with an opening of about 5 Angstroms in diameter and is positively charged.1 Publication

<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 bacterial microcompartments protein family. CcmK subfamily.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105HKE, Bacteria
COG4577, LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_064903_5_0_3

Identification of Orthologs from Complete Genome Data

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OMAi
ESWVIIP

Database of Orthologous Groups

More...
OrthoDBi
1802372at2

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
3.30.70.1710, 1 hit

HAMAP database of protein families

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HAMAPi
MF_00854, CcmK, 1 hit

Integrated resource of protein families, domains and functional sites

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InterProi
View protein in InterPro
IPR020808, Bact_microcomp_CS
IPR037233, CcmK-like_sf
IPR000249, Microcompartment_bac

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00936, BMC, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00877, BMC, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF143414, SSF143414, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS01139, BMC_1, 1 hit
PS51930, BMC_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.

Q31RK2-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSQQAIGSLE TKGFPPILAA ADAMVKAGRI TIVSYMRAGS ARFAVNIRGD
60 70 80 90 100
VSEVKTAMDA GIEAAKNTPG GTLETWVIIP RPHENVEAVF PIGFGPEVEQ
110
YRLSAEGTGS GRR
Length:113
Mass (Da):11,946
Last modified:December 6, 2005 - 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:iA961559E472C2545
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
CP000100 Genomic DNA Translation: ABB56317.1

NCBI Reference Sequences

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RefSeqi
WP_011243539.1, NC_007604.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
ABB56317; ABB56317; Synpcc7942_0285

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
syf:Synpcc7942_0285

<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
CP000100 Genomic DNA Translation: ABB56317.1
RefSeqiWP_011243539.1, NC_007604.1

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
4OX6X-ray1.34A/B1-113[»]
SMRiQ31RK2
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

STRINGi1140.Synpcc7942_0285

Proteomic databases

PRIDEiQ31RK2

Genome annotation databases

EnsemblBacteriaiABB56317; ABB56317; Synpcc7942_0285
KEGGisyf:Synpcc7942_0285

Phylogenomic databases

eggNOGiENOG4105HKE, Bacteria
COG4577, LUCA
HOGENOMiCLU_064903_5_0_3
OMAiESWVIIP
OrthoDBi1802372at2

Enzyme and pathway databases

BioCyciSYNEL:SYNPCC7942_0285-MONOMER

Family and domain databases

Gene3Di3.30.70.1710, 1 hit
HAMAPiMF_00854, CcmK, 1 hit
InterProiView protein in InterPro
IPR020808, Bact_microcomp_CS
IPR037233, CcmK-like_sf
IPR000249, Microcompartment_bac
PfamiView protein in Pfam
PF00936, BMC, 1 hit
SMARTiView protein in SMART
SM00877, BMC, 1 hit
SUPFAMiSSF143414, SSF143414, 1 hit
PROSITEiView protein in PROSITE
PS01139, BMC_1, 1 hit
PS51930, BMC_2, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

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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 nameiCCMK4_SYNE7
<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: Q31RK2
<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: October 7, 2020
Last sequence update: December 6, 2005
Last modified: April 7, 2021
This is version 69 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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