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A4XF23 (MAND_NOVAD) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 47. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
D-mannonate dehydratase

Short name=ManD
EC=4.2.1.8
Alternative name(s):
RspA homolog
Gene names
Name:manD
Ordered Locus Names:Saro_3675
Encoded onPlasmid pNL2 Ref.1
OrganismNovosphingobium aromaticivorans (strain DSM 12444 / F199) [Complete proteome] [HAMAP]
Taxonomic identifier279238 [NCBI]
Taxonomic lineageBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeNovosphingobium

Protein attributes

Sequence length402 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the dehydration of D-mannonate. Has no detectable activity with a panel of 70 other acid sugars (in vitro). Ref.2 Ref.3

Catalytic activity

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

Cofactor

Binds 1 Mg2+ ion per subunit. Ref.2 Ref.3

Pathway

Carbohydrate metabolism; pentose and glucuronate interconversion.

Subunit structure

Homotetramer. Ref.2

Sequence similarities

Belongs to the mandelate racemase/muconate lactonizing enzyme family. GalD subfamily.

Biophysicochemical properties

Kinetic parameters:

kcat is 1.3 sec(-1) with D-mannonate. Ref.2 Ref.3

Ontologies

Keywords
   Biological processCarbohydrate metabolism
   LigandMagnesium
Metal-binding
   Molecular functionLyase
   Technical term3D-structure
Complete proteome
Plasmid
Gene Ontology (GO)
   Biological_processcellular amino acid catabolic process

Inferred from electronic annotation. Source: InterPro

   Molecular_functioncatalytic activity

Inferred from electronic annotation. Source: InterPro

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 402402D-mannonate dehydratase
PRO_0000429873

Sites

Active site1591Proton donor/acceptor Probable
Active site2121Proton donor/acceptor Probable
Metal binding2101Magnesium
Metal binding2361Magnesium
Metal binding2621Magnesium
Binding site371Substrate
Binding site1221Substrate
Binding site2621Substrate
Binding site2831Substrate
Binding site3121Substrate
Binding site3161Substrate
Binding site3391Substrate
Site3141Important for activity and substrate specificity; Ala is observed in family members with high D-mannonate dehydratase activity that have no activity with D-gluconate

Experimental info

Mutagenesis1471R → A: Abolishes catalytic activity. Ref.2
Mutagenesis1471R → K: Decreases catalytic activity. Ref.2
Mutagenesis1591Y → F: Abolishes catalytic activity. Ref.2
Mutagenesis161 – 1699VGRGKLYYE → AGAGGAGAG: Abolishes catalytic activity. Ref.3
Mutagenesis2121H → N: Abolishes catalytic activity. Ref.2
Mutagenesis2711K → E: No effect on catalytic activity. Ref.2
Mutagenesis2831R → A: Abolishes catalytic activity. Ref.2
Mutagenesis3121H → N: Abolishes catalytic activity. Ref.2
Mutagenesis3141A → P: Decreases catalytic activity. Ref.3
Mutagenesis3391E → Q: Abolishes catalytic activity. Ref.2

Sequences

Sequence LengthMass (Da)Tools
A4XF23 [UniParc].

Last modified May 29, 2007. Version 1.
Checksum: E22007CDD0538750

FASTA40245,244
        10         20         30         40         50         60 
MKITAARVII TCPGRNFVTL KIETDQGVYG IGDATLNGRE LSVVAYLQEH VAPCLIGMDP 

        70         80         90        100        110        120 
RRIEDIWQYV YRGAYWRRGP VTMRAIAAVD MALWDIKAKM AGMPLYQLLG GRSRDGIMVY 

       130        140        150        160        170        180 
GHANGSDIAE TVEAVGHYID MGYKAIRAQT GVPGIKDAYG VGRGKLYYEP ADASLPSVTG 

       190        200        210        220        230        240 
WDTRKALNYV PKLFEELRKT YGFDHHLLHD GHHRYTPQEA ANLGKMLEPY QLFWLEDCTP 

       250        260        270        280        290        300 
AENQEAFRLV RQHTVTPLAV GEIFNTIWDA KDLIQNQLID YIRATVVGAG GLTHLRRIAD 

       310        320        330        340        350        360 
LASLYQVRTG CHGATDLSPV TMGCALHFDT WVPNFGIQEY MRHTEETDAV FPHDYWFEKG 

       370        380        390        400 
ELFVGETPGH GVDIDEELAA KYPYKPAYLP VARLEDGTMW NW 

« Hide

References

« Hide 'large scale' references
[1]"Complete sequence of plasmid pNL2 of Novosphingobium aromaticivorans DSM 12444."
US DOE Joint Genome Institute
Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Chertkov O., Han C., Thomson S., Schmutz J., Larimer F., Land M., Kyrpides N. expand/collapse author list , Ivanova N., Fredrickson J., Romine M.F., Richardson P.
Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: DSM 12444 / F199.
[2]"Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans."
Rakus J.F., Fedorov A.A., Fedorov E.V., Glasner M.E., Vick J.E., Babbitt P.C., Almo S.C., Gerlt J.A.
Biochemistry 46:12896-12908(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH D-MANNONIC ACID AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, SUBUNIT, ACTIVE SITE, MUTAGENESIS OF ARG-147; TYR-159; HIS-212; LYS-271; ARG-283; HIS-312 AND GLU-339.
Strain: DSM 12444 / F199.
[3]"Discovery of function in the enolase superfamily: D-mannonate and D-gluconate dehydratases in the D-mannonate dehydratase subgroup."
Wichelecki D.J., Balthazor B.M., Chau A.C., Vetting M.W., Fedorov A.A., Fedorov E.V., Lukk T., Patskovsky Y.V., Stead M.B., Hillerich B.S., Seidel R.D., Almo S.C., Gerlt J.A.
Biochemistry 53:2722-2731(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.25 ANGSTROMS) IN COMPLEX D-MANNONIC ACID AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF 161-VAL--GLU-169 AND ALA-314.
Strain: DSM 12444 / F199.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000677 Genomic DNA. Translation: ABP64534.1.
RefSeqYP_001166060.1. NC_009427.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalA4XF23.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING279238.Saro_3675.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABP64534; ABP64534; Saro_3675.
GeneID5077823.
KEGGnar:Saro_3675.
PATRIC22790486. VBINovAro50627_3893.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG4948.
HOGENOMHOG000113758.
KOK08323.
OMANQRAFEI.
OrthoDBEOG6SBSZM.

Enzyme and pathway databases

BioCycNARO279238:GHBU-3686-MONOMER.
UniPathwayUPA00246.

Family and domain databases

Gene3D3.20.20.120. 1 hit.
3.30.390.10. 1 hit.
InterProIPR029065. Enolase_C-like.
IPR029017. Enolase_N_like.
IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
IPR013342. Mandelate_racemase_C.
IPR013341. Mandelate_racemase_N.
IPR001354. MR_MLE.
[Graphical view]
PANTHERPTHR13794. PTHR13794. 1 hit.
PfamPF01188. MR_MLE. 1 hit.
PF02746. MR_MLE_N. 1 hit.
[Graphical view]
SMARTSM00922. MR_MLE. 1 hit.
[Graphical view]
SUPFAMSSF51604. SSF51604. 1 hit.
SSF54826. SSF54826. 1 hit.
PROSITEPS00908. MR_MLE_1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceA4XF23.

Entry information

Entry nameMAND_NOVAD
AccessionPrimary (citable) accession number: A4XF23
Entry history
Integrated into UniProtKB/Swiss-Prot: July 9, 2014
Last sequence update: May 29, 2007
Last modified: July 9, 2014
This is version 47 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways