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Protein

GDP-mannose 4,6-dehydratase

Gene

gmd

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Status
Reviewed-Annotation score: Annotation score: 5 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 annotation1 Publication

Catalytic activityi

GDP-alpha-D-mannose = GDP-4-dehydro-alpha-D-rhamnose + H2O.UniRule annotation1 Publication

Cofactori

NADP+UniRule annotation1 Publication

Pathwayi: lipopolysaccharide biosynthesis

This protein is involved in the pathway lipopolysaccharide biosynthesis, which is part of Bacterial outer membrane biogenesis.1 Publication
View all proteins of this organism that are known to be involved in the pathway lipopolysaccharide biosynthesis and in Bacterial outer membrane biogenesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei36NADPUniRule annotation1 Publication1
Active sitei126UniRule annotation1
Active sitei128NucleophileUniRule annotation1
Active sitei150NucleophileUniRule annotation1
Binding sitei154NADPUniRule annotation1 Publication1
Binding sitei180NADPUniRule annotation1 Publication1
Binding sitei185NADPUniRule annotation1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi11 – 14NADPUniRule annotation1 Publication4
Nucleotide bindingi59 – 60NADPUniRule annotation1 Publication2
Nucleotide bindingi81 – 85NADPUniRule annotation1 Publication5

GO - Molecular functioni

GO - Biological processi

  • GDP-mannose metabolic process Source: InterPro
  • lipopolysaccharide biosynthetic process Source: PseudoCAP
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Lipopolysaccharide biosynthesis

Keywords - Ligandi

NADP

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-12848.
BRENDAi4.2.1.47. 5087.
UniPathwayiUPA00030.

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:gmdUniRule annotation
Synonyms:gca
Ordered Locus Names:PA5453
OrganismiPseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Taxonomic identifieri208964 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000002438 Componenti: Chromosome

Organism-specific databases

PseudoCAPiPA5453.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002017151 – 323GDP-mannose 4,6-dehydrataseAdd BLAST323

Proteomic databases

PaxDbiQ51366.
PRIDEiQ51366.

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

STRINGi208964.PA5453.

Structurei

Secondary structure

1323
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 8Combined sources5
Turni9 – 11Combined sources3
Helixi13 – 24Combined sources12
Beta strandi28 – 33Combined sources6
Helixi42 – 46Combined sources5
Helixi50 – 52Combined sources3
Beta strandi53 – 57Combined sources5
Helixi63 – 73Combined sources11
Beta strandi76 – 80Combined sources5
Helixi87 – 90Combined sources4
Helixi94 – 101Combined sources8
Helixi103 – 115Combined sources13
Beta strandi119 – 126Combined sources8
Helixi127 – 130Combined sources4
Beta strandi134 – 138Combined sources5
Helixi149 – 168Combined sources20
Beta strandi172 – 177Combined sources6
Helixi190 – 202Combined sources13
Beta strandi209 – 212Combined sources4
Beta strandi217 – 219Combined sources3
Helixi223 – 235Combined sources13
Beta strandi236 – 238Combined sources3
Beta strandi242 – 244Combined sources3
Beta strandi249 – 251Combined sources3
Helixi252 – 261Combined sources10
Turni262 – 264Combined sources3
Helixi267 – 269Combined sources3
Beta strandi271 – 273Combined sources3
Helixi275 – 277Combined sources3
Helixi291 – 297Combined sources7
Helixi305 – 322Combined sources18

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1RPNX-ray2.15A/B/C/D1-323[»]
ProteinModelPortaliQ51366.
SMRiQ51366.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ51366.

Family & Domainsi

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.
InParanoidiQ51366.
KOiK01711.
OMAiDYQHRTG.
PhylomeDBiQ51366.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00955. GDP_Man_dehydratase. 1 hit.
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.

Q51366-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTRSALVTGI TGQDGAYLAK LLLEKGYRVH GLVARRSSDT RWRLRELGIE
60 70 80 90 100
GDIQYEDGDM ADACSVQRAV IKAQPQEVYN LAAQSFVGAS WNQPVTTGVV
110 120 130 140 150
DGLGVTHLLE AIRQFSPETR FYQASTSEMF GLIQAERQDE NTPFYPRSPY
160 170 180 190 200
GVAKLYGHWI TVNYRESFGL HASSGILFNH ESPLRGIEFV TRKVTDAVAR
210 220 230 240 250
IKLGKQQELR LGNVDAKRDW GFAGDYVEAM WLMLQQDKAD DYVVATGVTT
260 270 280 290 300
TVRDMCQIAF EHVGLDYRDF LKIDPAFFRP AEVDVLLGNP AKAQRVLGWK
310 320
PRTSLDELIR MMVEADLRRV SRE
Length:323
Mass (Da):36,399
Last modified:December 8, 2000 - v2
Checksum:i6C2BCC27D00D97E0
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti153A → V in AAC44117 (PubMed:8548534).Curated1
Sequence conflicti167S → N in AAC44117 (PubMed:8548534).Curated1
Sequence conflicti216A → V in AAC44117 (PubMed:8548534).Curated1
Sequence conflicti223A → G in AAC44117 (PubMed:8548534).Curated1
Sequence conflicti247G → V in AAC44117 (PubMed:8548534).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18320 Genomic DNA. Translation: AAC44117.1.
AE004091 Genomic DNA. Translation: AAG08838.1.
PIRiG82964.
RefSeqiNP_254140.1. NC_002516.2.
WP_003096890.1. NZ_ASJY01000837.1.

Genome annotation databases

EnsemblBacteriaiAAG08838; AAG08838; PA5453.
GeneIDi883089.
KEGGipae:PA5453.
PATRICi19845789. VBIPseAer58763_5716.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18320 Genomic DNA. Translation: AAC44117.1.
AE004091 Genomic DNA. Translation: AAG08838.1.
PIRiG82964.
RefSeqiNP_254140.1. NC_002516.2.
WP_003096890.1. NZ_ASJY01000837.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1RPNX-ray2.15A/B/C/D1-323[»]
ProteinModelPortaliQ51366.
SMRiQ51366.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi208964.PA5453.

Proteomic databases

PaxDbiQ51366.
PRIDEiQ51366.

Protocols and materials databases

DNASUi883089.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAG08838; AAG08838; PA5453.
GeneIDi883089.
KEGGipae:PA5453.
PATRICi19845789. VBIPseAer58763_5716.

Organism-specific databases

PseudoCAPiPA5453.

Phylogenomic databases

eggNOGiENOG4105C0K. Bacteria.
COG1089. LUCA.
HOGENOMiHOG000168003.
InParanoidiQ51366.
KOiK01711.
OMAiDYQHRTG.
PhylomeDBiQ51366.

Enzyme and pathway databases

UniPathwayiUPA00030.
BioCyciMetaCyc:MONOMER-12848.
BRENDAi4.2.1.47. 5087.

Miscellaneous databases

EvolutionaryTraceiQ51366.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_00955. GDP_Man_dehydratase. 1 hit.
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...

Entry informationi

Entry nameiGM4D_PSEAE
AccessioniPrimary (citable) accession number: Q51366
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: December 8, 2000
Last modified: November 2, 2016
This is version 117 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, 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.