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UniProtKB - Q46893 (ISPD_ECOLI)

Entry version 176 (23 Feb 2022)
Sequence version 3 (23 Jan 2007)
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Protein

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

Gene

ispD

Organism
Escherichia coli (strain K12)
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

Catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP).

Miscellaneous

There are no coordination bonds that occur between IspD and magnesium in any of the complexes examined to date.

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<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

Mg2+, Mn2+, Co2+

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>pH dependencei

Optimum pH is 8.3.

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: isopentenyl diphosphate biosynthesis via DXP pathway

This protein is involved in step 2 of the subpathway that synthesizes isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate. This subpathway is part of the pathway isopentenyl diphosphate biosynthesis via DXP pathway, which is itself part of Isoprenoid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes isopentenyl diphosphate from 1-deoxy-D-xylulose 5-phosphate, the pathway isopentenyl diphosphate biosynthesis via DXP pathway and in Isoprenoid biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei20Transition state stabilizer1 Publication1
Sitei27Transition state stabilizer1 Publication1
Sitei157Positions MEP for the nucleophilic attack1 Publication1
Sitei213Positions MEP for the nucleophilic attack1 Publication1

<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

Molecular functionNucleotidyltransferase, Transferase
Biological processIsoprene biosynthesis
LigandCobalt, Magnesium, Manganese

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:G7423-MONOMER

BRENDA Comprehensive Enzyme Information System

More...BRENDAi		2.7.7.60, 2026

SABIO-RK: Biochemical Reaction Kinetics Database

More...SABIO-RKi		Q46893

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...UniPathwayi		UPA00056;UER00093

<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:
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (EC:2.7.7.60)
Alternative name(s):
4-diphosphocytidyl-2C-methyl-D-erythritol synthase
CDP-ME synthase
MEP cytidylyltransferase
Short name:
MCT
<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:ispD
Synonyms:ygbP
Ordered Locus Names:b2747, JW2717
<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>OrganismiEscherichia coli (strain K12)
<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 identifieri83333 [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 › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<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
  • UP000000318 <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
  • UP000000625 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

<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

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>Mutagenesisi27K → A or S: Strong decrease in activity. 1 Publication1
Mutagenesisi140T → I: Loss of activity. 1 Publication1
Mutagenesisi191E → K: Loss of activity. 1 Publication1
Mutagenesisi213K → S: Decrease in activity. 1 Publication1

Chemistry databases

Drug and drug target database

More...DrugBanki		DB03687, 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol
DB03854, Cadaverine
DB02431, Cytidine-5'-Triphosphate

<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 <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemoved
<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_00000755722 – 2362-C-methyl-D-erythritol 4-phosphate cytidylyltransferaseAdd BLAST235

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		Q46893

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

More...PaxDbi		Q46893

PRoteomics IDEntifications database

More...PRIDEi		Q46893

<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

Homodimer.

1 Publication

GO - Molecular functioni

Complete GO annotation on QuickGO ...

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		4262280, 173 interactors

Protein interaction database and analysis system

More...IntActi		Q46893, 2 interactors

STRING: functional protein association networks

More...STRINGi		511145.b2747

<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

1236
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

More...SMRi		Q46893

Database of comparative protein structure models

More...ModBasei		Search...

Protein Data Bank in Europe - Knowledge Base

More...PDBe-KBi		Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...EvolutionaryTracei		Q46893

<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

<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 IspD/TarI cytidylyltransferase family. IspD subfamily.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG1211, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_061281_3_1_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		Q46893

Database for complete collections of gene phylogenies

More...PhylomeDBi		Q46893

Family and domain databases

Conserved Domains Database

More...CDDi		cd02516, CDP-ME_synthetase, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.90.550.10, 1 hit

HAMAP database of protein families

More...HAMAPi		MF_00108, IspD, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR001228, IspD
IPR034683, IspD/TarI
IPR018294, ISPD_synthase_CS
IPR029044, Nucleotide-diphossugar_trans

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01128, IspD, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF53448, SSF53448, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR00453, ispD, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS01295, ISPD, 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.

<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 in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

Q46893-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MATTHLDVCA VVPAAGFGRR MQTECPKQYL SIGNQTILEH SVHALLAHPR 
        60         70         80         90        100
VKRVVIAISP GDSRFAQLPL ANHPQITVVD GGDERADSVL AGLKAAGDAQ 
       110        120        130        140        150
WVLVHDAARP CLHQDDLARL LALSETSRTG GILAAPVRDT MKRAEPGKNA 
       160        170        180        190        200
IAHTVDRNGL WHALTPQFFP RELLHDCLTR ALNEGATITD EASALEYCGF 
       210        220        230 
HPQLVEGRAD NIKVTRPEDL ALAEFYLTRT IHQENT
Length:236
Mass (Da):25,737
Last modified:January 23, 2007 - v3
<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:i6AD26690AC2CF201
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
AF230736 Genomic DNA Translation: AAF43207.1
AB037143 Genomic DNA Translation: BAA90761.1
U29579 Genomic DNA Translation: AAA69257.1
U00096 Genomic DNA Translation: AAC75789.1
AP009048 Genomic DNA Translation: BAE76824.1

Protein sequence database of the Protein Information Resource

More...PIRi		G65055

NCBI Reference Sequences

More...RefSeqi		NP_417227.1, NC_000913.3
WP_000246138.1, NZ_STEB01000027.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC75789; AAC75789; b2747
BAE76824; BAE76824; BAE76824

Database of genes from NCBI RefSeq genomes

More...GeneIDi		948269

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW2717
eco:b2747

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.3993

<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
AF230736 Genomic DNA Translation: AAF43207.1
AB037143 Genomic DNA Translation: BAA90761.1
U29579 Genomic DNA Translation: AAA69257.1
U00096 Genomic DNA Translation: AAC75789.1
AP009048 Genomic DNA Translation: BAE76824.1
PIRiG65055
RefSeqiNP_417227.1, NC_000913.3
WP_000246138.1, NZ_STEB01000027.1

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
1H3MX-ray2.40A/B2-236[»]
1I52X-ray1.50A1-236[»]
1INIX-ray1.82A1-236[»]
1INJX-ray1.55A1-236[»]
1VGTX-ray1.80A/B2-236[»]
1VGUX-ray2.80A/B2-236[»]
3N9WX-ray1.90A/B2-236[»]
SMRiQ46893
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4262280, 173 interactors
IntActiQ46893, 2 interactors
STRINGi511145.b2747

Chemistry databases

DrugBankiDB03687, 4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol
DB03854, Cadaverine
DB02431, Cytidine-5'-Triphosphate

Proteomic databases

jPOSTiQ46893
PaxDbiQ46893
PRIDEiQ46893

Genome annotation databases

EnsemblBacteriaiAAC75789; AAC75789; b2747
BAE76824; BAE76824; BAE76824
GeneIDi948269
KEGGiecj:JW2717
eco:b2747
PATRICifig|1411691.4.peg.3993

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...EchoBASEi		EB2913

Phylogenomic databases

eggNOGiCOG1211, Bacteria
HOGENOMiCLU_061281_3_1_6
InParanoidiQ46893
PhylomeDBiQ46893

Enzyme and pathway databases

UniPathwayiUPA00056;UER00093
BioCyciEcoCyc:G7423-MONOMER
BRENDAi2.7.7.60, 2026
SABIO-RKiQ46893

Miscellaneous databases

EvolutionaryTraceiQ46893

Protein Ontology

More...PROi		PR:Q46893

Family and domain databases

CDDicd02516, CDP-ME_synthetase, 1 hit
Gene3Di3.90.550.10, 1 hit
HAMAPiMF_00108, IspD, 1 hit
InterProiView protein in InterPro
IPR001228, IspD
IPR034683, IspD/TarI
IPR018294, ISPD_synthase_CS
IPR029044, Nucleotide-diphossugar_trans
PfamiView protein in Pfam
PF01128, IspD, 1 hit
SUPFAMiSSF53448, SSF53448, 1 hit
TIGRFAMsiTIGR00453, ispD, 1 hit
PROSITEiView protein in PROSITE
PS01295, ISPD, 1 hit

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 nameiISPD_ECOLI
<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: Q46893
Secondary accession number(s): Q2MA82
<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: November 1, 1997
Last sequence update: January 23, 2007
Last modified: February 23, 2022
This is version 176 of the entry and version 3 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, Direct protein sequencing, Reference proteome

Documents

  1. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families
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