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Protein

D-galactarolactone cycloisomerase

Gene

gci

Organism
Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens (strain C58))
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the ring opening of D-galactaro-1,4-lactone to yield 5-keto-4-deoxy-D-glucarate (KDG) via a beta-elimination reaction. This is a step in the oxidative degradation pathway of D-galacturonate, which allows A.tumefaciens to utilize D-galacturonate as a sole carbon source. To a lesser extent, can also use D-glucaro-1,4-lactone as substrate to produce KDG, but cannot use D-galactaro-1,5-lactone, D-glucaro-6,3-lactone and linear D-glucarate.2 Publications

Catalytic activityi

D-glucaro-1,4-lactone = 5-dehydro-4-deoxy-D-glucarate.2 Publications
D-galactaro-1,4-lactone = 5-dehydro-4-deoxy-D-glucarate.2 Publications

Cofactori

Mg2+1 Publication

pH dependencei

Optimum pH is 8.5.1 Publication

Pathwayi: D-galacturonate degradation via prokaryotic oxidative pathway

This protein is involved in the pathway D-galacturonate degradation via prokaryotic oxidative pathway, which is part of Carbohydrate acid metabolism.1 Publication
View all proteins of this organism that are known to be involved in the pathway D-galacturonate degradation via prokaryotic oxidative pathway and in Carbohydrate acid metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi194Magnesium1
Metal bindingi220Magnesium1
Metal bindingi246Magnesium1
Sitei269Increases basicity of active site HisBy similarity1
Active sitei296Proton acceptorBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciAGRO:ATU3139-MONOMER.
MetaCyc:MONOMER-18901.
UniPathwayiUPA01050.

Names & Taxonomyi

Protein namesi
Recommended name:
D-galactarolactone cycloisomerase (EC:5.5.1.272 Publications)
Gene namesi
Name:gci
Ordered Locus Names:Atu3139
OrganismiAgrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens (strain C58))
Taxonomic identifieri176299 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupAgrobacteriumAgrobacterium tumefaciens complex
Proteomesi
  • UP000000813 Componenti: Chromosome linear

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004294331 – 378D-galactarolactone cycloisomeraseAdd BLAST378

Interactioni

Subunit structurei

Homooctamer.2 Publications

Protein-protein interaction databases

STRINGi176299.Atu3139.

Structurei

Secondary structure

1378
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 20Combined sources18
Beta strandi25 – 38Combined sources14
Beta strandi43 – 48Combined sources6
Helixi52 – 63Combined sources12
Turni64 – 68Combined sources5
Helixi74 – 84Combined sources11
Helixi85 – 88Combined sources4
Helixi93 – 113Combined sources21
Helixi117 – 120Combined sources4
Beta strandi127 – 134Combined sources8
Helixi144 – 157Combined sources14
Beta strandi161 – 166Combined sources6
Helixi171 – 185Combined sources15
Turni186 – 188Combined sources3
Beta strandi189 – 194Combined sources6
Helixi201 – 211Combined sources11
Helixi212 – 214Combined sources3
Beta strandi217 – 220Combined sources4
Helixi228 – 237Combined sources10
Beta strandi238 – 240Combined sources3
Beta strandi242 – 244Combined sources3
Helixi250 – 259Combined sources10
Beta strandi264 – 266Combined sources3
Turni270 – 274Combined sources5
Helixi275 – 289Combined sources15
Helixi301 – 313Combined sources13
Beta strandi328 – 331Combined sources4
Helixi337 – 340Combined sources4
Beta strandi342 – 344Combined sources3
Beta strandi352 – 354Combined sources3
Beta strandi358 – 360Combined sources3
Helixi367 – 372Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4GGBX-ray2.00A1-378[»]
4HPNX-ray1.60A1-378[»]
ProteinModelPortaliA9CEQ8.
SMRiA9CEQ8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105CXK. Bacteria.
COG4948. LUCA.
HOGENOMiHOG000113756.
KOiK18983.
OMAiFAPHLWA.

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. 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.

A9CEQ8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKITAVRTHL LEHRLDTPFE SASMRFDRRA HVLVEIECDD GTVGWGECLG
60 70 80 90 100
PARPNAAVVQ AYSGWLIGQD PRQTEKIWAV LYNALRDQGQ RGLSLTALSG
110 120 130 140 150
IDIALWDIKG KHYGASISML LGGRWRESVR AYATGSFKRD NVDRVSDNAS
160 170 180 190 200
EMAERRAEGF HACKIKIGFG VEEDLRVIAA VREAIGPDMR LMIDANHGYT
210 220 230 240 250
VTEAITLGDR AAGFGIDWFE EPVVPEQLDA YARVRAGQPI PVAGGETWHG
260 270 280 290 300
RYGMWQALSA GAVDILQPDL CGCGGFSEIQ KIATLATLHG VRIVPHVWGT
310 320 330 340 350
GVQIAAALQF MAAMTPDPVR VNPIEPIMEF DRTHNPFRQA VLREPLEAVN
360 370
GVVTIPDGPG LGIEINRDAL TEFRMPDP
Length:378
Mass (Da):41,456
Last modified:January 15, 2008 - v1
Checksum:i3B4EC2C7877DDCD6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE007870 Genomic DNA. Translation: AAK90247.1.
PIRiAE2942.
E98340.
RefSeqiNP_357462.1. NC_003063.2.
WP_010972789.1. NC_003063.2.

Genome annotation databases

EnsemblBacteriaiAAK90247; AAK90247; Atu3139.
GeneIDi1134941.
KEGGiatu:Atu3139.
PATRICi20815744. VBIAgrTum91616_2984.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE007870 Genomic DNA. Translation: AAK90247.1.
PIRiAE2942.
E98340.
RefSeqiNP_357462.1. NC_003063.2.
WP_010972789.1. NC_003063.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4GGBX-ray2.00A1-378[»]
4HPNX-ray1.60A1-378[»]
ProteinModelPortaliA9CEQ8.
SMRiA9CEQ8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi176299.Atu3139.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAK90247; AAK90247; Atu3139.
GeneIDi1134941.
KEGGiatu:Atu3139.
PATRICi20815744. VBIAgrTum91616_2984.

Phylogenomic databases

eggNOGiENOG4105CXK. Bacteria.
COG4948. LUCA.
HOGENOMiHOG000113756.
KOiK18983.
OMAiFAPHLWA.

Enzyme and pathway databases

UniPathwayiUPA01050.
BioCyciAGRO:ATU3139-MONOMER.
MetaCyc:MONOMER-18901.

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. 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 nameiGCI_AGRFC
AccessioniPrimary (citable) accession number: A9CEQ8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 11, 2014
Last sequence update: January 15, 2008
Last modified: November 2, 2016
This is version 57 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, 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.