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Protein

GDP-mannose 4,6-dehydratase

Gene

rfbD

Organism
Aquifex aeolicus (strain VF5)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of GDP-D-mannose to GDP-4-dehydro-6-deoxy-D-mannose.UniRule annotation

Catalytic activityi

GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H2O.UniRule annotation

Cofactori

NADP+UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei127 – 1271UniRule annotation
Active sitei129 – 1291NucleophileUniRule annotation
Active sitei151 – 1511NucleophileUniRule annotation
Binding sitei151 – 1511NADPCombined sources
Binding sitei155 – 1551NADPUniRule annotationCombined sources
Binding sitei181 – 1811NADPUniRule annotationCombined sources
Binding sitei186 – 1861NADPUniRule annotationCombined sources

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi10 – 156NADPUniRule annotation
Nucleotide bindingi14 – 152NADPCombined sources
Nucleotide bindingi34 – 363NADPCombined sources
Nucleotide bindingi60 – 612NADPUniRule annotationCombined sources
Nucleotide bindingi82 – 865NADPUniRule annotationCombined sources

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

LyaseUniRule annotation

Keywords - Ligandi

NADPUniRule annotationCombined sources, Nucleotide-bindingCombined sources

Enzyme and pathway databases

BioCyciAAEO224324:GJBH-773-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
GDP-mannose 4,6-dehydrataseUniRule annotation (EC:4.2.1.47UniRule annotation)
Alternative name(s):
GDP-D-mannose dehydrataseUniRule annotation
Gene namesi
Name:rfbDImported
Synonyms:gmdUniRule annotation
Ordered Locus Names:aq_1082Imported
OrganismiAquifex aeolicus (strain VF5)Imported
Taxonomic identifieri224324 [NCBI]
Taxonomic lineageiBacteriaAquificaeAquificalesAquificaceaeAquifex
Proteomesi
  • UP000000798 Componenti: Chromosome

Interactioni

Protein-protein interaction databases

STRINGi224324.aq_1082.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Z1MX-ray2.00A/B/C/D1-345[»]
2Z95X-ray2.60A/B/C/D1-345[»]
ProteinModelPortaliO67175.
SMRiO67175. Positions 3-340.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO67175.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini7 – 330324NAD(P)-bd_domInterPro annotationAdd
BLAST

Sequence similaritiesi

Belongs to the NAD(P)-dependent epimerase/dehydratase family. GDP-mannose 4,6-dehydratase subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C0K. Bacteria.
COG1089. LUCA.
HOGENOMiHOG000168003.
InParanoidiO67175.
KOiK01711.
OMAiSDMMKAD.
OrthoDBiEOG6V7BNH.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00955. GDP_Man_dehydratase.
InterProiIPR006368. GDP_Man_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF16363. GDP_Man_Dehyd. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01472. gmd. 1 hit.

Sequencei

Sequence statusi: Complete.

O67175-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGKRALITG IRGQDGAYLA KLLLEKGYEV YGADRRSGEF ASWRLKELGI
60 70 80 90 100
ENDVKIIHMD LLEFSNIIRT IEKVQPDEVY NLAAQSFVGV SFEQPILTAE
110 120 130 140 150
VDAIGVLRIL EALRTVKPDT KFYQASTSEM FGKVQEIPQT EKTPFYPRSP
160 170 180 190 200
YAVAKLFGHW ITVNYREAYN MFACSGILFN HESPLRGIEF VTRKITYSLA
210 220 230 240 250
RIKYGLQDKL VLGNLNAKRD WGYAPEYVEA MWLMMQQPEP DDYVIATGET
260 270 280 290 300
HTVREFVEKA AKIAGFDIEW VGEGINEKGI DRNTGKVIVE VSEEFFRPAE
310 320 330 340
VDILVGNPEK AMKKLGWKPR TTFDELVEIM MEADLKRVRD REVSV
Length:345
Mass (Da):39,338
Last modified:August 1, 1998 - v1
Checksum:iCEEC5FFD4CA2710A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC07133.1.
PIRiD70393.
RefSeqiNP_213738.1. NC_000918.1.
WP_010880676.1. NC_000918.1.

Genome annotation databases

EnsemblBacteriaiAAC07133; AAC07133; aq_1082.
GeneIDi1193809.
KEGGiaae:aq_1082.
PATRICi20959444. VBIAquAeo85532_0842.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC07133.1.
PIRiD70393.
RefSeqiNP_213738.1. NC_000918.1.
WP_010880676.1. NC_000918.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2Z1MX-ray2.00A/B/C/D1-345[»]
2Z95X-ray2.60A/B/C/D1-345[»]
ProteinModelPortaliO67175.
SMRiO67175. Positions 3-340.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224324.aq_1082.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC07133; AAC07133; aq_1082.
GeneIDi1193809.
KEGGiaae:aq_1082.
PATRICi20959444. VBIAquAeo85532_0842.

Phylogenomic databases

eggNOGiENOG4105C0K. Bacteria.
COG1089. LUCA.
HOGENOMiHOG000168003.
InParanoidiO67175.
KOiK01711.
OMAiSDMMKAD.
OrthoDBiEOG6V7BNH.

Enzyme and pathway databases

BioCyciAAEO224324:GJBH-773-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO67175.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00955. GDP_Man_dehydratase.
InterProiIPR006368. GDP_Man_deHydtase.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF16363. GDP_Man_Dehyd. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01472. gmd. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: VF5Imported.
  2. "Crystal Structure of GDP-D-Mannose Dehydratase from Aquifex aeolicus VF5."
    Niwa H., Kuramitsu S., Yokoyama S.
    Submitted (MAY-2007) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH NADP.

Entry informationi

Entry nameiO67175_AQUAE
AccessioniPrimary (citable) accession number: O67175
Entry historyi
Integrated into UniProtKB/TrEMBL: August 1, 1998
Last sequence update: August 1, 1998
Last modified: April 13, 2016
This is version 102 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources, Complete proteome, Reference proteomeImported

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.