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Protein

Rhamnulose-1-phosphate aldolase

Gene

rhaD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible cleavage of L-rhamnulose-1-phosphate to dihydroxyacetone phosphate (DHAP) and L-lactaldehyde (PubMed:12962479). Also catalyzes the dephosphorylation of phospho-serine in vitro (PubMed:25848029).2 Publications

Catalytic activityi

L-rhamnulose 1-phosphate = glycerone phosphate + (S)-lactaldehyde.1 Publication

Cofactori

Zn2+2 PublicationsNote: Binds 1 zinc ion per subunit.2 Publications

Kineticsi

  1. KM=0.48 mM for L-rhamnulose 1-phosphate (at 37 degrees Celsius)1 Publication

    Pathwayi: L-rhamnose degradation

    This protein is involved in step 3 of the subpathway that synthesizes glycerone phosphate from L-rhamnose.
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. L-rhamnose isomerase (rhaA)
    2. L-Rhamnulokinase (rhaB)
    3. Rhamnulose-1-phosphate aldolase (rhaD)
    This subpathway is part of the pathway L-rhamnose degradation, which is itself part of Carbohydrate degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes glycerone phosphate from L-rhamnose, the pathway L-rhamnose degradation and in Carbohydrate degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei1172 Publications1
    Metal bindingi141Zinc2 Publications1
    Metal bindingi143Zinc2 Publications1
    Metal bindingi212Zinc2 Publications1

    GO - Molecular functioni

    • identical protein binding Source: EcoCyc
    • metal ion binding Source: UniProtKB-KW
    • rhamnulose-1-phosphate aldolase activity Source: EcoCyc

    GO - Biological processi

    • pentose catabolic process Source: GO_Central
    • rhamnose catabolic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Rhamnose metabolism

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:RHAMNULPALDOL-MONOMER.
    ECOL316407:JW3873-MONOMER.
    MetaCyc:RHAMNULPALDOL-MONOMER.
    BRENDAi4.1.2.19. 2026.
    UniPathwayiUPA00541; UER00603.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Rhamnulose-1-phosphate aldolase (EC:4.1.2.191 Publication)
    Gene namesi
    Name:rhaD
    Synonyms:rhuA
    Ordered Locus Names:b3902, JW3873
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11866. rhaD.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi28R → A or S: Severe loss of enzymatic activity. 1 Publication1
    Mutagenesisi29N → A: Severe loss of enzymatic activity. 1 Publication1
    Mutagenesisi117E → Q: Loss of enzymatic activity. 1 Publication1
    Mutagenesisi171E → S, A or Q: Loss of enzymatic activity. 1 Publication1
    Mutagenesisi192E → A: No effect on enzymatic activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00002096571 – 274Rhamnulose-1-phosphate aldolaseAdd BLAST274

    Proteomic databases

    PaxDbiP32169.
    PRIDEiP32169.

    Expressioni

    Inductioni

    Induced by L-rhamnose via the RhaR-RhaS regulatory cascade. Binding of the cAMP receptor protein (CRP) is required for full expression.2 Publications

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    GO - Molecular functioni

    • identical protein binding Source: EcoCyc

    Protein-protein interaction databases

    IntActiP32169. 7 interactors.
    STRINGi511145.b3902.

    Structurei

    Secondary structure

    1274
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi4 – 6Combined sources3
    Helixi8 – 22Combined sources15
    Beta strandi31 – 36Combined sources6
    Helixi39 – 42Combined sources4
    Helixi43 – 48Combined sources6
    Beta strandi54 – 57Combined sources4
    Helixi63 – 65Combined sources3
    Beta strandi69 – 74Combined sources6
    Helixi79 – 81Combined sources3
    Turni82 – 84Combined sources3
    Helixi86 – 89Combined sources4
    Beta strandi90 – 95Combined sources6
    Beta strandi99 – 107Combined sources9
    Turni109 – 111Combined sources3
    Helixi113 – 115Combined sources3
    Helixi118 – 131Combined sources14
    Turni132 – 134Combined sources3
    Beta strandi138 – 142Combined sources5
    Helixi145 – 150Combined sources6
    Turni151 – 153Combined sources3
    Helixi158 – 167Combined sources10
    Helixi172 – 175Combined sources4
    Beta strandi180 – 182Combined sources3
    Beta strandi188 – 190Combined sources3
    Helixi191 – 201Combined sources11
    Beta strandi205 – 209Combined sources5
    Turni210 – 212Combined sources3
    Beta strandi213 – 220Combined sources8
    Helixi221 – 243Combined sources23
    Helixi256 – 263Combined sources8
    Helixi269 – 272Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1GT7X-ray2.70A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T1-274[»]
    1OJRX-ray1.35A1-274[»]
    2UYUX-ray1.96A/E1-274[»]
    2UYVX-ray2.20A/B/C/D1-274[»]
    2V29X-ray2.03A/B1-274[»]
    2V2AX-ray1.75A1-274[»]
    2V2BX-ray1.50A1-274[»]
    2V9EX-ray1.58A/B1-272[»]
    2V9FX-ray2.10A1-272[»]
    2V9GX-ray2.70A/B/C/D1-274[»]
    2V9IX-ray1.80A/B1-273[»]
    2V9LX-ray1.23A1-274[»]
    2V9MX-ray1.30A/B1-274[»]
    2V9NX-ray1.40A/B/C/D1-274[»]
    2V9OX-ray1.95A/E1-274[»]
    ProteinModelPortaliP32169.
    SMRiP32169.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP32169.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105C9J. Bacteria.
    COG0235. LUCA.
    HOGENOMiHOG000279628.
    InParanoidiP32169.
    KOiK01629.
    OMAiSHFMSHI.
    PhylomeDBiP32169.

    Family and domain databases

    Gene3Di3.40.225.10. 1 hit.
    HAMAPiMF_00770. RhaD. 1 hit.
    InterProiIPR001303. Aldolase_II/adducin_N.
    IPR013447. Rhamnulose-1-P_Aldolase.
    [Graphical view]
    PfamiPF00596. Aldolase_II. 1 hit.
    [Graphical view]
    SMARTiSM01007. Aldolase_II. 1 hit.
    [Graphical view]
    SUPFAMiSSF53639. SSF53639. 1 hit.
    TIGRFAMsiTIGR02624. rhamnu_1P_ald. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P32169-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MQNITQSWFV QGMIKATTDA WLKGWDERNG GNLTLRLDDA DIAPYHDNFH
    60 70 80 90 100
    QQPRYIPLSQ PMPLLANTPF IVTGSGKFFR NVQLDPAANL GIVKVDSDGA
    110 120 130 140 150
    GYHILWGLTN EAVPTSELPA HFLSHCERIK ATNGKDRVIM HCHATNLIAL
    160 170 180 190 200
    TYVLENDTAV FTRQLWEGST ECLVVFPDGV GILPWMVPGT DEIGQATAQE
    210 220 230 240 250
    MQKHSLVLWP FHGVFGSGPT LDETFGLIDT AEKSAQVLVK VYSMGGMKQT
    260 270
    ISREELIALG KRFGVTPLAS ALAL
    Length:274
    Mass (Da):30,145
    Last modified:October 1, 1993 - v1
    Checksum:iF9FF0BE156F4E63D
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X60472 Genomic DNA. Translation: CAA43003.1.
    L19201 Genomic DNA. Translation: AAB03035.1.
    U00096 Genomic DNA. Translation: AAC76884.1.
    AP009048 Genomic DNA. Translation: BAE77407.1.
    PIRiC48649.
    RefSeqiNP_418338.1. NC_000913.3.
    WP_001179745.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76884; AAC76884; b3902.
    BAE77407; BAE77407; BAE77407.
    GeneIDi948401.
    KEGGiecj:JW3873.
    eco:b3902.
    PATRICi32123313. VBIEscCol129921_4017.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X60472 Genomic DNA. Translation: CAA43003.1.
    L19201 Genomic DNA. Translation: AAB03035.1.
    U00096 Genomic DNA. Translation: AAC76884.1.
    AP009048 Genomic DNA. Translation: BAE77407.1.
    PIRiC48649.
    RefSeqiNP_418338.1. NC_000913.3.
    WP_001179745.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1GT7X-ray2.70A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T1-274[»]
    1OJRX-ray1.35A1-274[»]
    2UYUX-ray1.96A/E1-274[»]
    2UYVX-ray2.20A/B/C/D1-274[»]
    2V29X-ray2.03A/B1-274[»]
    2V2AX-ray1.75A1-274[»]
    2V2BX-ray1.50A1-274[»]
    2V9EX-ray1.58A/B1-272[»]
    2V9FX-ray2.10A1-272[»]
    2V9GX-ray2.70A/B/C/D1-274[»]
    2V9IX-ray1.80A/B1-273[»]
    2V9LX-ray1.23A1-274[»]
    2V9MX-ray1.30A/B1-274[»]
    2V9NX-ray1.40A/B/C/D1-274[»]
    2V9OX-ray1.95A/E1-274[»]
    ProteinModelPortaliP32169.
    SMRiP32169.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiP32169. 7 interactors.
    STRINGi511145.b3902.

    Proteomic databases

    PaxDbiP32169.
    PRIDEiP32169.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76884; AAC76884; b3902.
    BAE77407; BAE77407; BAE77407.
    GeneIDi948401.
    KEGGiecj:JW3873.
    eco:b3902.
    PATRICi32123313. VBIEscCol129921_4017.

    Organism-specific databases

    EchoBASEiEB1812.
    EcoGeneiEG11866. rhaD.

    Phylogenomic databases

    eggNOGiENOG4105C9J. Bacteria.
    COG0235. LUCA.
    HOGENOMiHOG000279628.
    InParanoidiP32169.
    KOiK01629.
    OMAiSHFMSHI.
    PhylomeDBiP32169.

    Enzyme and pathway databases

    UniPathwayiUPA00541; UER00603.
    BioCyciEcoCyc:RHAMNULPALDOL-MONOMER.
    ECOL316407:JW3873-MONOMER.
    MetaCyc:RHAMNULPALDOL-MONOMER.
    BRENDAi4.1.2.19. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP32169.
    PROiP32169.

    Family and domain databases

    Gene3Di3.40.225.10. 1 hit.
    HAMAPiMF_00770. RhaD. 1 hit.
    InterProiIPR001303. Aldolase_II/adducin_N.
    IPR013447. Rhamnulose-1-P_Aldolase.
    [Graphical view]
    PfamiPF00596. Aldolase_II. 1 hit.
    [Graphical view]
    SMARTiSM01007. Aldolase_II. 1 hit.
    [Graphical view]
    SUPFAMiSSF53639. SSF53639. 1 hit.
    TIGRFAMsiTIGR02624. rhamnu_1P_ald. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiRHAD_ECOLI
    AccessioniPrimary (citable) accession number: P32169
    Secondary accession number(s): Q2M8J9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1993
    Last sequence update: October 1, 1993
    Last modified: November 2, 2016
    This is version 130 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. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    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

    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 one 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.