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Protein

L-rhamnonate dehydratase

Gene

rhmD

Organism
Delftia acidovorans (strain DSM 14801 / SPH-1)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Catalyzes the dehydration of L-rhamnonate to 2-keto-3-deoxy-L-rhamnonate (KDR).UniRule annotation

Catalytic activityi

L-rhamnonate = 2-dehydro-3-deoxy-L-rhamnonate + H2O.UniRule annotation

Cofactori

Mg2+UniRule annotationNote: Binds 1 Mg2+ ion per subunit.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei23SubstrateUniRule annotation1
Binding sitei49SubstrateUniRule annotation1
Metal bindingi215MagnesiumUniRule annotation1
Metal bindingi241MagnesiumUniRule annotation1
Metal bindingi269MagnesiumUniRule annotation1
Sitei292Increases basicity of active site HisUniRule annotation1
Active sitei319Proton acceptorUniRule annotation1
Binding sitei339SubstrateUniRule annotation1
Sitei339Transition state stabilizerUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Magnesium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
L-rhamnonate dehydrataseUniRule annotation (EC:4.2.1.90UniRule annotation)
Short name:
RhamDUniRule annotation
Gene namesi
Name:rhmDUniRule annotation
Ordered Locus Names:Daci_0291
OrganismiDelftia acidovorans (strain DSM 14801 / SPH-1)
Taxonomic identifieri398578 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeDelftia
Proteomesi
  • UP000000784 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003516901 – 395L-rhamnonate dehydrataseAdd BLAST395

Interactioni

Subunit structurei

Homooctamer; tetramer of dimers.UniRule annotation

Protein-protein interaction databases

STRINGi398578.Daci_0291.

Structurei

3D structure databases

ProteinModelPortaliA9BQY2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the mandelate racemase/muconate lactonizing enzyme family. RhamD subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CXK. Bacteria.
COG4948. LUCA.
HOGENOMiHOG000113755.
KOiK12661.

Family and domain databases

Gene3Di3.20.20.120. 1 hit.
3.30.390.10. 1 hit.
HAMAPiMF_01288. Rhamnon_dehydrat. 1 hit.
InterProiIPR029065. Enolase_C-like.
IPR029017. Enolase_N-like.
IPR023444. L-Rhamnon_dehydrat.
IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
IPR013342. Mandelate_racemase_C.
IPR013341. Mandelate_racemase_N_dom.
IPR001354. MR/MLE/MAL.
[Graphical view]
PANTHERiPTHR13794. PTHR13794. 1 hit.
PfamiPF13378. MR_MLE_C. 1 hit.
PF02746. MR_MLE_N. 1 hit.
[Graphical view]
SMARTiSM00922. MR_MLE. 1 hit.
[Graphical view]
SUPFAMiSSF51604. SSF51604. 1 hit.
SSF54826. SSF54826. 1 hit.
PROSITEiPS00908. MR_MLE_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A9BQY2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTQIPTIKQV RAFTLKGGGA DYHDQSDGHW IDDHIATPMA KYPEYRQSRR
60 70 80 90 100
SFGINVLGTL VVEIEDSAGR VGFAVTTGGE PAAYIVEKHL ARFLEGARVT
110 120 130 140 150
DIERIWDQMY LSTLYYGRKG IVINTISGVD LALWDLLGKV RGEPVHQLLG
160 170 180 190 200
GAVRDELQFY ATGARPDLAQ KMGFIGGKMP LHHGPAEGEE GLRRNLQELA
210 220 230 240 250
TMRERVGPDF WLMLDCWMSL DVNYATRLAQ GAQAHGLKWI EEALPPDDYW
260 270 280 290 300
GYAALRKNVP TGMLVTTGEH EATRWGFRQL LEMGCCDIIQ PDVGWCGGIT
310 320 330 340 350
ELLKISALAD AHQALVIPHG SSVYSYHFVA TRHNSPFAEF LMMAPKADEV
360 370 380 390
VPMFHPQLLG EPVPVNGRMR LSALDRPGFG VELNPECALH RPYTH
Length:395
Mass (Da):43,944
Last modified:October 14, 2008 - v2
Checksum:i96CD5CB9833E4E1F
GO

Sequence cautioni

The sequence ABX32937 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000884 Genomic DNA. Translation: ABX32937.1. Different initiation.
RefSeqiWP_016452099.1. NC_010002.1.

Genome annotation databases

EnsemblBacteriaiABX32937; ABX32937; Daci_0291.
GeneIDi24115216.
KEGGidac:Daci_0291.
PATRICi21634395. VBIDelAci41351_0303.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000884 Genomic DNA. Translation: ABX32937.1. Different initiation.
RefSeqiWP_016452099.1. NC_010002.1.

3D structure databases

ProteinModelPortaliA9BQY2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi398578.Daci_0291.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABX32937; ABX32937; Daci_0291.
GeneIDi24115216.
KEGGidac:Daci_0291.
PATRICi21634395. VBIDelAci41351_0303.

Phylogenomic databases

eggNOGiENOG4105CXK. Bacteria.
COG4948. LUCA.
HOGENOMiHOG000113755.
KOiK12661.

Family and domain databases

Gene3Di3.20.20.120. 1 hit.
3.30.390.10. 1 hit.
HAMAPiMF_01288. Rhamnon_dehydrat. 1 hit.
InterProiIPR029065. Enolase_C-like.
IPR029017. Enolase_N-like.
IPR023444. L-Rhamnon_dehydrat.
IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
IPR013342. Mandelate_racemase_C.
IPR013341. Mandelate_racemase_N_dom.
IPR001354. MR/MLE/MAL.
[Graphical view]
PANTHERiPTHR13794. PTHR13794. 1 hit.
PfamiPF13378. MR_MLE_C. 1 hit.
PF02746. MR_MLE_N. 1 hit.
[Graphical view]
SMARTiSM00922. MR_MLE. 1 hit.
[Graphical view]
SUPFAMiSSF51604. SSF51604. 1 hit.
SSF54826. SSF54826. 1 hit.
PROSITEiPS00908. MR_MLE_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRHMD_DELAS
AccessioniPrimary (citable) accession number: A9BQY2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 14, 2008
Last sequence update: October 14, 2008
Last modified: November 2, 2016
This is version 49 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Reaction proceeds via a syn dehydration.UniRule annotation

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. 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.