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Entry version 153 (02 Jun 2021)
Sequence version 2 (24 Nov 2009)
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Protein

L-rhamnonate dehydratase

Gene

rhmD

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 dehydration of L-rhamnonate to 2-keto-3-deoxy-L-rhamnonate (KDR). Can also dehydrate L-lyxonate, L-mannonate and D-gulonate, although less efficiently, but not 2-keto-4-hydroxyheptane-1,7-dioate.

1 Publication

Miscellaneous

Reaction proceeds via a syn dehydration.

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">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+By similarityNote: Binds 1 Mg2+ ion per subunit.By similarity

<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>Kineticsi

The catalytic efficiency observed with L-rhamnonate as substrate is 70- and 16-fold higher than that observed with L-lyxonate and L-mannonate, respectively.
  1. KM=0.15 mM for L-rhamnonate1 Publication
  2. KM=2.0 mM for L-lyxonate1 Publication
  3. KM=0.15 mM for L-mannonate1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei29Substrate1
Binding sitei55SubstrateBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi222MagnesiumBy similarity1
Metal bindingi248MagnesiumBy similarity1
Metal bindingi276MagnesiumBy similarity1
<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>Sitei298Increases basicity of active site HisBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei325Proton acceptor1
Binding sitei345SubstrateBy similarity1
Sitei345Transition state stabilizerBy similarity1

<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

Molecular functionLyase
LigandMagnesium, Metal-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:G7160-MONOMER
MetaCyc:G7160-MONOMER

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
4.2.1.90, 2165

<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_and_taxonomy_section">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:
L-rhamnonate dehydratase (EC:4.2.1.90)
Short name:
RhamD
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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:rhmD
Synonyms:yfaW
Ordered Locus Names:b2247, JW2241
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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_and_taxonomy_section">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_and_taxonomy_section">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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">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_manual">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 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_and_biotech_section">'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>Mutagenesisi29H → N: Loss of activity due to absence of substrate binding. 1 Publication1
Mutagenesisi277H → N: 35-fold decrease in activity. 59-fold decrease in substrate affinity. 1 Publication1
Mutagenesisi325H → N: Loss of activity. 2-fold decrease in substrate affinity. 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_00001712621 – 401L-rhamnonate dehydrataseAdd BLAST401

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P77215

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

More...
PaxDbi
P77215

PRoteomics IDEntifications database

More...
PRIDEi
P77215

<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_section">'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_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homooctamer; tetramer of dimers.

1 Publication

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
4261221, 144 interactors

Database of interacting proteins

More...
DIPi
DIP-11955N

Protein interaction database and analysis system

More...
IntActi
P77215, 11 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b2247

<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

1401
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
P77215

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
P77215

<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

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG4948, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_030273_1_0_6

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P77215

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P77215

Family and domain databases

Conserved Domains Database

More...
CDDi
cd03327, MR_like_2, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.20.20.120, 1 hit
3.30.390.10, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_01288, Rhamnon_dehydrat, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR036849, Enolase-like_C_sf
IPR029017, Enolase-like_N
IPR029065, Enolase_C-like
IPR023444, L-Rhamnon_dehydrat
IPR018110, Mandel_Rmase/mucon_lact_enz_CS
IPR013342, Mandelate_racemase_C
IPR013341, Mandelate_racemase_N_dom

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF13378, MR_MLE_C, 1 hit
PF02746, MR_MLE_N, 1 hit

Structure-Function Linkage Database

More...
SFLDi
SFLDF00006, rhamnonate_dehydratase, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00922, MR_MLE, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF51604, SSF51604, 1 hit
SSF54826, SSF54826, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00908, MR_MLE_1, 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_length">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_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">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.

P77215-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTLPKIKQVR AWFTGGATAE KGAGGGDYHD QGANHWIDDH IATPMSKYRD
60 70 80 90 100
YEQSRQSFGI NVLGTLVVEV EAENGQTGFA VSTAGEMGCF IVEKHLNRFI
110 120 130 140 150
EGKCVSDIKL IHDQMLSATL YYSGSGGLVM NTISCVDLAL WDLFGKVVGL
160 170 180 190 200
PVYKLLGGAV RDEIQFYATG ARPDLAKEMG FIGGKMPTHW GPHDGDAGIR
210 220 230 240 250
KDAAMVADMR EKCGEDFWLM LDCWMSQDVN YATKLAHACA PYNLKWIEEC
260 270 280 290 300
LPPQQYESYR ELKRNAPVGM MVTSGEHHGT LQSFRTLSET GIDIMQPDVG
310 320 330 340 350
WCGGLTTLVE IAAIAKSRGQ LVVPHGSSVY SHHAVITFTN TPFSEFLMTS
360 370 380 390 400
PDCSTMRPQF DPILLNEPVP VNGRIHKSVL DKPGFGVELN RDCNLKRPYS

H
Length:401
Mass (Da):44,226
Last modified:November 24, 2009 - v2
<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:i4622CE539229AD58
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence BAA16071 differs from that shown. Reason: Erroneous initiation.Curated

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
U00096 Genomic DNA Translation: AAC75307.2
AP009048 Genomic DNA Translation: BAA16071.1 Different initiation.

Protein sequence database of the Protein Information Resource

More...
PIRi
E64995

NCBI Reference Sequences

More...
RefSeqi
NP_416750.2, NC_000913.3
WP_001319848.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC75307; AAC75307; b2247
BAA16071; BAA16071; BAA16071

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
945881

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW2241
eco:b2247

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|511145.12.peg.2338

<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
U00096 Genomic DNA Translation: AAC75307.2
AP009048 Genomic DNA Translation: BAA16071.1 Different initiation.
PIRiE64995
RefSeqiNP_416750.2, NC_000913.3
WP_001319848.1, NZ_LN832404.1

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
2I5QX-ray2.10A/B1-401[»]
SMRiP77215
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGRIDi4261221, 144 interactors
DIPiDIP-11955N
IntActiP77215, 11 interactors
STRINGi511145.b2247

Proteomic databases

jPOSTiP77215
PaxDbiP77215
PRIDEiP77215

Genome annotation databases

EnsemblBacteriaiAAC75307; AAC75307; b2247
BAA16071; BAA16071; BAA16071
GeneIDi945881
KEGGiecj:JW2241
eco:b2247
PATRICifig|511145.12.peg.2338

Organism-specific databases

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

More...
EchoBASEi
EB3838

Phylogenomic databases

eggNOGiCOG4948, Bacteria
HOGENOMiCLU_030273_1_0_6
InParanoidiP77215
PhylomeDBiP77215

Enzyme and pathway databases

BioCyciEcoCyc:G7160-MONOMER
MetaCyc:G7160-MONOMER
BRENDAi4.2.1.90, 2165

Miscellaneous databases

EvolutionaryTraceiP77215

Protein Ontology

More...
PROi
PR:P77215

Family and domain databases

CDDicd03327, MR_like_2, 1 hit
Gene3Di3.20.20.120, 1 hit
3.30.390.10, 1 hit
HAMAPiMF_01288, Rhamnon_dehydrat, 1 hit
InterProiView protein in InterPro
IPR036849, Enolase-like_C_sf
IPR029017, Enolase-like_N
IPR029065, Enolase_C-like
IPR023444, L-Rhamnon_dehydrat
IPR018110, Mandel_Rmase/mucon_lact_enz_CS
IPR013342, Mandelate_racemase_C
IPR013341, Mandelate_racemase_N_dom
PfamiView protein in Pfam
PF13378, MR_MLE_C, 1 hit
PF02746, MR_MLE_N, 1 hit
SFLDiSFLDF00006, rhamnonate_dehydratase, 1 hit
SMARTiView protein in SMART
SM00922, MR_MLE, 1 hit
SUPFAMiSSF51604, SSF51604, 1 hit
SSF54826, SSF54826, 1 hit
PROSITEiView protein in PROSITE
PS00908, MR_MLE_1, 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 nameiRHMD_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: P77215
<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_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 24, 2009
Last modified: June 2, 2021
This is version 153 of the entry and version 2 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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