Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

D-mannonate dehydratase

Gene

manD

Organism
Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the dehydration of D-mannonate. Has no detectable activity with a panel of 70 other acid sugars (in vitro).2 Publications

Catalytic activityi

D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O.2 Publications

Cofactori

Mg2+2 PublicationsNote: Binds 1 Mg2+ ion per subunit.2 Publications

Kineticsi

kcat is 1.3 sec(-1) with D-mannonate.2 Publications

Manual assertion based on experiment ini

      Pathwayi: pentose and glucuronate interconversion

      This protein is involved in the pathway pentose and glucuronate interconversion, which is part of Carbohydrate metabolism.
      View all proteins of this organism that are known to be involved in the pathway pentose and glucuronate interconversion and in Carbohydrate metabolism.

      Sites

      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      Binding sitei37Substrate1
      Binding sitei122Substrate1
      Active sitei159Proton donor/acceptor1 Publication1
      Metal bindingi210Magnesium1 Publication1
      Active sitei212Proton donor/acceptor1 Publication1
      Metal bindingi236Magnesium1 Publication1
      Metal bindingi262Magnesium1 Publication1
      Binding sitei262Substrate1
      Binding sitei283Substrate1
      Binding sitei312Substrate1
      Sitei314Important for activity and substrate specificity; Ala is observed in family members with high D-mannonate dehydratase activity that have no activity with D-gluconate1
      Binding sitei316Substrate1
      Binding sitei339Substrate1

      GO - Molecular functioni

      • gluconate dehydratase activity Source: UniProtKB
      • magnesium ion binding Source: UniProtKB
      • mannonate dehydratase activity Source: UniProtKB

      GO - Biological processi

      • carbohydrate catabolic process Source: UniProtKB
      • cellular amino acid catabolic process Source: InterPro
      Complete GO annotation...

      Keywords - Molecular functioni

      Lyase

      Keywords - Biological processi

      Carbohydrate metabolism

      Keywords - Ligandi

      Magnesium, Metal-binding

      Enzyme and pathway databases

      UniPathwayiUPA00246.

      Names & Taxonomyi

      Protein namesi
      Recommended name:
      D-mannonate dehydratase (EC:4.2.1.8)
      Short name:
      ManD
      Alternative name(s):
      RspA homolog
      Gene namesi
      Name:manD
      Ordered Locus Names:Saro_3675
      Encoded oniPlasmid pNL21 Publication
      OrganismiNovosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CIP 105152 / NBRC 16084 / F199)
      Taxonomic identifieri279238 [NCBI]
      Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeNovosphingobium
      Proteomesi
      • UP000009134 Componenti: Plasmid pNL2

      Pathology & Biotechi

      Mutagenesis

      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      Mutagenesisi147R → A: Abolishes catalytic activity. 1 Publication1
      Mutagenesisi147R → K: Decreases catalytic activity. 1 Publication1
      Mutagenesisi159Y → F: Abolishes catalytic activity. 1 Publication1
      Mutagenesisi161 – 169VGRGKLYYE → AGAGGAGAG: Abolishes catalytic activity. 1 Publication9
      Mutagenesisi212H → N: Abolishes catalytic activity. 1 Publication1
      Mutagenesisi271K → E: No effect on catalytic activity. 1 Publication1
      Mutagenesisi283R → A: Abolishes catalytic activity. 1 Publication1
      Mutagenesisi312H → N: Abolishes catalytic activity. 1 Publication1
      Mutagenesisi314A → P: Decreases catalytic activity. 1 Publication1
      Mutagenesisi339E → Q: Abolishes catalytic activity. 1 Publication1

      PTM / Processingi

      Molecule processing

      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      ChainiPRO_00004298731 – 402D-mannonate dehydrataseAdd BLAST402

      Interactioni

      Subunit structurei

      Homotetramer.1 Publication

      Structurei

      Secondary structure

      1402
      Legend: HelixTurnBeta strandPDB Structure known for this area
      Show more details
      Feature keyPosition(s)DescriptionActionsGraphical viewLength
      Beta strandi3 – 11Combined sources9
      Beta strandi13 – 15Combined sources3
      Beta strandi17 – 27Combined sources11
      Beta strandi29 – 33Combined sources5
      Helixi40 – 49Combined sources10
      Helixi51 – 55Combined sources5
      Helixi63 – 73Combined sources11
      Helixi80 – 101Combined sources22
      Helixi105 – 109Combined sources5
      Beta strandi115 – 127Combined sources13
      Helixi128 – 140Combined sources13
      Beta strandi144 – 150Combined sources7
      Beta strandi173 – 175Combined sources3
      Beta strandi178 – 181Combined sources4
      Helixi183 – 187Combined sources5
      Helixi190 – 201Combined sources12
      Beta strandi203 – 210Combined sources8
      Helixi217 – 227Combined sources11
      Helixi228 – 230Combined sources3
      Beta strandi233 – 237Combined sources5
      Helixi244 – 247Combined sources4
      Helixi248 – 253Combined sources6
      Beta strandi258 – 260Combined sources3
      Helixi267 – 269Combined sources3
      Helixi271 – 275Combined sources5
      Beta strandi280 – 282Combined sources3
      Turni286 – 290Combined sources5
      Helixi291 – 304Combined sources14
      Beta strandi308 – 311Combined sources4
      Helixi319 – 331Combined sources13
      Beta strandi335 – 339Combined sources5
      Helixi345 – 350Combined sources6
      Beta strandi353 – 358Combined sources6
      Beta strandi361 – 364Combined sources4
      Beta strandi368 – 372Combined sources5
      Helixi376 – 379Combined sources4
      Beta strandi391 – 394Combined sources4

      3D structure databases

      Select the link destinations:
      PDBei
      RCSB PDBi
      PDBji
      Links Updated
      PDB entryMethodResolution (Å)ChainPositionsPDBsum
      2QJJX-ray1.80A/B/C/D1-402[»]
      2QJMX-ray2.20A/B/C/D1-402[»]
      2QJNX-ray2.00A/B/C/D1-402[»]
      4K1WX-ray1.65A/B/C/D1-402[»]
      4K8GX-ray1.25A1-402[»]
      ProteinModelPortaliA4XF23.
      SMRiA4XF23.
      ModBaseiSearch...
      MobiDBiSearch...

      Miscellaneous databases

      EvolutionaryTraceiA4XF23.

      Family & Domainsi

      Sequence similaritiesi

      Phylogenomic databases

      HOGENOMiHOG000113758.
      KOiK08323.
      OMAiNQRAFEI.
      OrthoDBiPOG091H0FES.

      Family and domain databases

      Gene3Di3.20.20.120. 1 hit.
      3.30.390.10. 1 hit.
      InterProiIPR029065. Enolase_C-like.
      IPR029017. Enolase_N-like.
      IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
      IPR013342. Mandelate_racemase_C.
      IPR013341. Mandelate_racemase_N_dom.
      IPR001354. MR/MLE/MAL.
      [Graphical view]
      PANTHERiPTHR13794. PTHR13794. 2 hits.
      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.

      A4XF23-1 [UniParc]FASTAAdd to basket

      « Hide

              10         20         30         40         50
      MKITAARVII TCPGRNFVTL KIETDQGVYG IGDATLNGRE LSVVAYLQEH
      60 70 80 90 100
      VAPCLIGMDP RRIEDIWQYV YRGAYWRRGP VTMRAIAAVD MALWDIKAKM
      110 120 130 140 150
      AGMPLYQLLG GRSRDGIMVY GHANGSDIAE TVEAVGHYID MGYKAIRAQT
      160 170 180 190 200
      GVPGIKDAYG VGRGKLYYEP ADASLPSVTG WDTRKALNYV PKLFEELRKT
      210 220 230 240 250
      YGFDHHLLHD GHHRYTPQEA ANLGKMLEPY QLFWLEDCTP AENQEAFRLV
      260 270 280 290 300
      RQHTVTPLAV GEIFNTIWDA KDLIQNQLID YIRATVVGAG GLTHLRRIAD
      310 320 330 340 350
      LASLYQVRTG CHGATDLSPV TMGCALHFDT WVPNFGIQEY MRHTEETDAV
      360 370 380 390 400
      FPHDYWFEKG ELFVGETPGH GVDIDEELAA KYPYKPAYLP VARLEDGTMW

      NW
      Length:402
      Mass (Da):45,244
      Last modified:May 29, 2007 - v1
      Checksum:iE22007CDD0538750
      GO

      Sequence databases

      Select the link destinations:
      EMBLi
      GenBanki
      DDBJi
      Links Updated
      CP000677 Genomic DNA. Translation: ABP64534.1.
      RefSeqiWP_011906920.1. NC_009427.1.

      Genome annotation databases

      EnsemblBacteriaiABP64534; ABP64534; Saro_3675.
      KEGGinar:Saro_3675.
      PATRICi22790486. VBINovAro50627_3893.

      Cross-referencesi

      Sequence databases

      Select the link destinations:
      EMBLi
      GenBanki
      DDBJi
      Links Updated
      CP000677 Genomic DNA. Translation: ABP64534.1.
      RefSeqiWP_011906920.1. NC_009427.1.

      3D structure databases

      Select the link destinations:
      PDBei
      RCSB PDBi
      PDBji
      Links Updated
      PDB entryMethodResolution (Å)ChainPositionsPDBsum
      2QJJX-ray1.80A/B/C/D1-402[»]
      2QJMX-ray2.20A/B/C/D1-402[»]
      2QJNX-ray2.00A/B/C/D1-402[»]
      4K1WX-ray1.65A/B/C/D1-402[»]
      4K8GX-ray1.25A1-402[»]
      ProteinModelPortaliA4XF23.
      SMRiA4XF23.
      ModBaseiSearch...
      MobiDBiSearch...

      Protocols and materials databases

      Structural Biology KnowledgebaseSearch...

      Genome annotation databases

      EnsemblBacteriaiABP64534; ABP64534; Saro_3675.
      KEGGinar:Saro_3675.
      PATRICi22790486. VBINovAro50627_3893.

      Phylogenomic databases

      HOGENOMiHOG000113758.
      KOiK08323.
      OMAiNQRAFEI.
      OrthoDBiPOG091H0FES.

      Enzyme and pathway databases

      UniPathwayiUPA00246.

      Miscellaneous databases

      EvolutionaryTraceiA4XF23.

      Family and domain databases

      Gene3Di3.20.20.120. 1 hit.
      3.30.390.10. 1 hit.
      InterProiIPR029065. Enolase_C-like.
      IPR029017. Enolase_N-like.
      IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
      IPR013342. Mandelate_racemase_C.
      IPR013341. Mandelate_racemase_N_dom.
      IPR001354. MR/MLE/MAL.
      [Graphical view]
      PANTHERiPTHR13794. PTHR13794. 2 hits.
      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 nameiMAND_NOVAD
      AccessioniPrimary (citable) accession number: A4XF23
      Entry historyi
      Integrated into UniProtKB/Swiss-Prot: July 9, 2014
      Last sequence update: May 29, 2007
      Last modified: November 2, 2016
      This is version 62 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, Plasmid, Reference proteome

      Documents

      1. PATHWAY comments
        Index of metabolic and biosynthesis pathways
      2. PDB cross-references
        Index of Protein Data Bank (PDB) cross-references
      3. 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.