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Protein

Aconitate hydratase B

Gene

acnB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the catabolism of short chain fatty acids (SCFA) via the tricarboxylic acid (TCA)(acetyl degradation route) and the 2-methylcitrate cycle I (propionate degradation route). Catalyzes the reversible isomerization of citrate to isocitrate via cis-aconitate. Also catalyzes the hydration of 2-methyl-cis-aconitate to yield (2R,3S)-2-methylisocitrate. The apo form of AcnB functions as a RNA-binding regulatory protein. During oxidative stress inactive AcnB apo-enzyme without iron sulfur clusters binds the acnB mRNA 3' UTRs (untranslated regions), stabilizes acnB mRNA and increases AcnB synthesis, thus mediating a post-transcriptional positive autoregulatory switch. AcnB also decreases the stability of the sodA transcript.7 Publications

Catalytic activityi

Citrate = isocitrate.1 Publication
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = (Z)-but-2-ene-1,2,3-tricarboxylate + H2O.1 Publication

Cofactori

[4Fe-4S] cluster1 PublicationNote: Binds 1 [4Fe-4S] cluster per subunit.1 Publication

Kineticsi

  1. KM=11 mM for citrate2 Publications
  2. KM=0.016 mM for cis-aconitate2 Publications
  3. KM=0.051 mM for isocitrate (using 0.01-0.8 mM substrate)2 Publications
  4. KM=19.7 mM for isocitrate (using 0.8-40 mM substrate)2 Publications
  5. KM=0.21 mM for (2R,3S)-2-methylisocitrate2 Publications
  1. Vmax=23.8 µmol/min/mg enzyme with citrate as substrate2 Publications
  2. Vmax=39.1 µmol/min/mg enzyme with cis-aconitate as substrate2 Publications
  3. Vmax=5.92 µmol/min/mg enzyme using 0.01-0.8 mM isocitrate as substrate2 Publications
  4. Vmax=57.8 µmol/min/mg enzyme using 0.8-40 mM isocitrate as substrate2 Publications

pH dependencei

Optimum pH is 7.4.2 Publications

Pathwayi: propanoate degradation

This protein is involved in the pathway propanoate degradation, which is part of Organic acid metabolism.1 Publication
View all proteins of this organism that are known to be involved in the pathway propanoate degradation and in Organic acid metabolism.

Pathwayi: tricarboxylic acid cycle

This protein is involved in step 2 of the subpathway that synthesizes isocitrate from oxaloacetate.1 Publication
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Citrate synthase (gltA)
  2. Aconitate hydratase B (acnB), 2-methylcitrate dehydratase (prpD), Aconitate hydratase A (acnA), 2-methylcitrate synthase (prpC)
This subpathway is part of the pathway tricarboxylic acid cycle, which is itself part of Carbohydrate metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes isocitrate from oxaloacetate, the pathway tricarboxylic acid cycle and in Carbohydrate metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei191Substrate1 Publication1
Binding sitei498Substrate1 Publication1
Metal bindingi710Iron-sulfur (4Fe-4S)1 Publication1
Metal bindingi769Iron-sulfur (4Fe-4S)1 Publication1
Metal bindingi772Iron-sulfur (4Fe-4S)1 Publication1
Binding sitei791Substrate1 Publication1
Binding sitei796Substrate1 Publication1

GO - Molecular functioni

  • 2-methylisocitrate dehydratase activity Source: EcoCyc
  • 4 iron, 4 sulfur cluster binding Source: EcoCyc
  • aconitate hydratase activity Source: EcoCyc
  • metal ion binding Source: UniProtKB-KW
  • mRNA 3'-UTR binding Source: EcoCyc
  • mRNA binding Source: EcoliWiki

GO - Biological processi

  • glyoxylate cycle Source: EcoliWiki
  • propionate catabolic process, 2-methylcitrate cycle Source: EcoCyc
  • regulation of translation Source: EcoCyc
  • tricarboxylic acid cycle Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Tricarboxylic acid cycle

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding, RNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:ACONITATEDEHYDRB-MONOMER.
ECOL316407:JW0114-MONOMER.
MetaCyc:ACONITATEDEHYDRB-MONOMER.
BRENDAi4.2.1.3. 2026.
SABIO-RKP36683.
UniPathwayiUPA00223; UER00718.
UPA00946.

Names & Taxonomyi

Protein namesi
Recommended name:
Aconitate hydratase B1 Publication (EC:4.2.1.31 Publication)
Short name:
ACN1 Publication
Short name:
Aconitase1 Publication
Alternative name(s):
(2R,3S)-2-methylisocitrate dehydratase1 Publication
(2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase1 Publication
2-methyl-cis-aconitate hydratase1 Publication (EC:4.2.1.991 Publication)
Iron-responsive protein-like1 Publication
Short name:
IRP-like1 Publication
RNA-binding protein1 Publication
Gene namesi
Name:acnB1 Publication
Synonyms:yacI, yacJ
Ordered Locus Names:b0118, JW0114
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12316. acnB.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene are more sensitive to peroxide stress. The acnAB double mutant does not grow on unsupplemented glucose minimal medium and does not respond under aerobic conditions to glutamate. The acnAB double mutant retains a low but significant aconitase activity.3 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi769C → S: Inhibits the dimer formation. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000766751 – 865Aconitate hydratase BAdd BLAST865

Proteomic databases

EPDiP36683.
PaxDbiP36683.
PRIDEiP36683.

2D gel databases

SWISS-2DPAGEP36683.

Interactioni

Subunit structurei

Monomer. AcnB can also form a homodimer. The monomer-homodimer transition is dependent on iron availability and the carboxymethylation of C-273 inhibits the dimer formation.3 Publications

Protein-protein interaction databases

BioGridi4261902. 8 interactors.
849264. 1 interactor.
DIPiDIP-9044N.
IntActiP36683. 15 interactors.
STRINGi511145.b0118.

Structurei

Secondary structure

1865
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi2 – 14Combined sources13
Helixi24 – 35Combined sources12
Helixi42 – 51Combined sources10
Helixi59 – 72Combined sources14
Helixi83 – 90Combined sources8
Helixi99 – 104Combined sources6
Helixi105 – 107Combined sources3
Turni109 – 111Combined sources3
Helixi112 – 120Combined sources9
Helixi128 – 137Combined sources10
Helixi141 – 151Combined sources11
Helixi154 – 157Combined sources4
Beta strandi166 – 178Combined sources13
Helixi179 – 182Combined sources4
Helixi185 – 190Combined sources6
Helixi194 – 197Combined sources4
Helixi198 – 200Combined sources3
Turni214 – 216Combined sources3
Helixi220 – 227Combined sources8
Beta strandi233 – 243Combined sources11
Helixi248 – 257Combined sources10
Beta strandi258 – 261Combined sources4
Beta strandi264 – 269Combined sources6
Beta strandi272 – 278Combined sources7
Helixi280 – 288Combined sources9
Beta strandi292 – 295Combined sources4
Beta strandi306 – 310Combined sources5
Turni311 – 314Combined sources4
Beta strandi315 – 318Combined sources4
Turni319 – 321Combined sources3
Beta strandi324 – 327Combined sources4
Helixi334 – 341Combined sources8
Helixi344 – 360Combined sources17
Helixi384 – 391Combined sources8
Turni392 – 394Combined sources3
Beta strandi409 – 413Combined sources5
Turni415 – 417Combined sources3
Helixi418 – 427Combined sources10
Beta strandi438 – 440Combined sources3
Beta strandi444 – 448Combined sources5
Helixi451 – 465Combined sources15
Turni466 – 468Combined sources3
Helixi479 – 483Combined sources5
Helixi484 – 486Combined sources3
Beta strandi492 – 497Combined sources6
Beta strandi503 – 507Combined sources5
Helixi512 – 521Combined sources10
Beta strandi531 – 538Combined sources8
Helixi546 – 559Combined sources14
Turni573 – 576Combined sources4
Beta strandi577 – 583Combined sources7
Helixi589 – 597Combined sources9
Helixi598 – 600Combined sources3
Turni601 – 603Combined sources3
Beta strandi605 – 609Combined sources5
Helixi613 – 632Combined sources20
Helixi638 – 653Combined sources16
Beta strandi667 – 673Combined sources7
Helixi674 – 676Combined sources3
Beta strandi681 – 683Combined sources3
Beta strandi691 – 693Combined sources3
Helixi694 – 696Combined sources3
Turni697 – 699Combined sources3
Beta strandi704 – 707Combined sources4
Helixi714 – 726Combined sources13
Beta strandi732 – 737Combined sources6
Helixi742 – 750Combined sources9
Helixi753 – 760Combined sources8
Helixi770 – 772Combined sources3
Beta strandi775 – 777Combined sources3
Beta strandi784 – 790Combined sources7
Beta strandi796 – 798Combined sources3
Beta strandi802 – 805Combined sources4
Helixi808 – 817Combined sources10
Helixi823 – 834Combined sources12
Helixi837 – 840Combined sources4
Helixi846 – 848Combined sources3
Helixi850 – 857Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1L5JX-ray2.40A/B1-865[»]
ProteinModelPortaliP36683.
SMRiP36683.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP36683.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni244 – 246Substrate binding1 Publication3
Regioni414 – 416Substrate binding1 Publication3

Sequence similaritiesi

Belongs to the aconitase/IPM isomerase family.Curated

Phylogenomic databases

eggNOGiENOG4107QIJ. Bacteria.
COG1049. LUCA.
HOGENOMiHOG000205991.
InParanoidiP36683.
KOiK01682.
OMAiHATTRPD.
PhylomeDBiP36683.

Family and domain databases

CDDicd01576. AcnB_Swivel. 1 hit.
Gene3Di3.20.19.10. 1 hit.
3.30.499.10. 2 hits.
3.40.1060.10. 1 hit.
InterProiIPR015931. Acnase/IPM_dHydase_lsu_aba_1/3.
IPR015937. Acoase/IPM_deHydtase.
IPR001030. Acoase/IPM_deHydtase_lsu_aba.
IPR015928. Aconitase/3IPM_dehydase_swvl.
IPR015932. Aconitase/IPMdHydase_lsu_aba_2.
IPR018136. Aconitase_4Fe-4S_BS.
IPR004406. Aconitase_B.
IPR015933. Aconitase_B_HEAT-like_dom.
IPR015929. Aconitase_B_swivel.
[Graphical view]
PANTHERiPTHR11670. PTHR11670. 1 hit.
PfamiPF00330. Aconitase. 1 hit.
PF06434. Aconitase_2_N. 1 hit.
PF11791. Aconitase_B_N. 1 hit.
[Graphical view]
PIRSFiPIRSF036687. AcnB. 1 hit.
SUPFAMiSSF52016. SSF52016. 1 hit.
SSF53732. SSF53732. 1 hit.
SSF74778. SSF74778. 1 hit.
TIGRFAMsiTIGR00117. acnB. 1 hit.
PROSITEiPS00450. ACONITASE_1. 1 hit.
PS01244. ACONITASE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P36683-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLEEYRKHVA ERAAEGIAPK PLDANQMAAL VELLKNPPAG EEEFLLDLLT
60 70 80 90 100
NRVPPGVDEA AYVKAGFLAA IAKGEAKSPL LTPEKAIELL GTMQGGYNIH
110 120 130 140 150
PLIDALDDAK LAPIAAKALS HTLLMFDNFY DVEEKAKAGN EYAKQVMQSW
160 170 180 190 200
ADAEWFLNRP ALAEKLTVTV FKVTGETNTD DLSPAPDAWS RPDIPLHALA
210 220 230 240 250
MLKNAREGIE PDQPGVVGPI KQIEALQQKG FPLAYVGDVV GTGSSRKSAT
260 270 280 290 300
NSVLWFMGDD IPHVPNKRGG GLCLGGKIAP IFFNTMEDAG ALPIEVDVSN
310 320 330 340 350
LNMGDVIDVY PYKGEVRNHE TGELLATFEL KTDVLIDEVR AGGRIPLIIG
360 370 380 390 400
RGLTTKAREA LGLPHSDVFR QAKDVAESDR GFSLAQKMVG RACGVKGIRP
410 420 430 440 450
GAYCEPKMTS VGSQDTTGPM TRDELKDLAC LGFSADLVMQ SFCHTAAYPK
460 470 480 490 500
PVDVNTHHTL PDFIMNRGGV SLRPGDGVIH SWLNRMLLPD TVGTGGDSHT
510 520 530 540 550
RFPIGISFPA GSGLVAFAAA TGVMPLDMPE SVLVRFKGKM QPGITLRDLV
560 570 580 590 600
HAIPLYAIKQ GLLTVEKKGK KNIFSGRILE IEGLPDLKVE QAFELTDASA
610 620 630 640 650
ERSAAGCTIK LNKEPIIEYL NSNIVLLKWM IAEGYGDRRT LERRIQGMEK
660 670 680 690 700
WLANPELLEA DADAEYAAVI DIDLADIKEP ILCAPNDPDD ARPLSAVQGE
710 720 730 740 750
KIDEVFIGSC MTNIGHFRAA GKLLDAHKGQ LPTRLWVAPP TRMDAAQLTE
760 770 780 790 800
EGYYSVFGKS GARIEIPGCS LCMGNQARVA DGATVVSTST RNFPNRLGTG
810 820 830 840 850
ANVFLASAEL AAVAALIGKL PTPEEYQTYV AQVDKTAVDT YRYLNFNQLS
860
QYTEKADGVI FQTAV
Length:865
Mass (Da):93,498
Last modified:November 1, 1997 - v3
Checksum:iFEC8AA5D2A9DD2BD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC73229.1.
AP009048 Genomic DNA. Translation: BAB96692.2.
U41560 Genomic DNA. Translation: AAC43710.1.
PIRiF64734.
RefSeqiNP_414660.1. NC_000913.3.
WP_001307570.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73229; AAC73229; b0118.
BAB96692; BAB96692; BAB96692.
GeneIDi944864.
KEGGiecj:JW0114.
eco:b0118.
PATRICi32115337. VBIEscCol129921_0120.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC73229.1.
AP009048 Genomic DNA. Translation: BAB96692.2.
U41560 Genomic DNA. Translation: AAC43710.1.
PIRiF64734.
RefSeqiNP_414660.1. NC_000913.3.
WP_001307570.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1L5JX-ray2.40A/B1-865[»]
ProteinModelPortaliP36683.
SMRiP36683.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261902. 8 interactors.
849264. 1 interactor.
DIPiDIP-9044N.
IntActiP36683. 15 interactors.
STRINGi511145.b0118.

2D gel databases

SWISS-2DPAGEP36683.

Proteomic databases

EPDiP36683.
PaxDbiP36683.
PRIDEiP36683.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73229; AAC73229; b0118.
BAB96692; BAB96692; BAB96692.
GeneIDi944864.
KEGGiecj:JW0114.
eco:b0118.
PATRICi32115337. VBIEscCol129921_0120.

Organism-specific databases

EchoBASEiEB2222.
EcoGeneiEG12316. acnB.

Phylogenomic databases

eggNOGiENOG4107QIJ. Bacteria.
COG1049. LUCA.
HOGENOMiHOG000205991.
InParanoidiP36683.
KOiK01682.
OMAiHATTRPD.
PhylomeDBiP36683.

Enzyme and pathway databases

UniPathwayiUPA00223; UER00718.
UPA00946.
BioCyciEcoCyc:ACONITATEDEHYDRB-MONOMER.
ECOL316407:JW0114-MONOMER.
MetaCyc:ACONITATEDEHYDRB-MONOMER.
BRENDAi4.2.1.3. 2026.
SABIO-RKP36683.

Miscellaneous databases

EvolutionaryTraceiP36683.
PROiP36683.

Family and domain databases

CDDicd01576. AcnB_Swivel. 1 hit.
Gene3Di3.20.19.10. 1 hit.
3.30.499.10. 2 hits.
3.40.1060.10. 1 hit.
InterProiIPR015931. Acnase/IPM_dHydase_lsu_aba_1/3.
IPR015937. Acoase/IPM_deHydtase.
IPR001030. Acoase/IPM_deHydtase_lsu_aba.
IPR015928. Aconitase/3IPM_dehydase_swvl.
IPR015932. Aconitase/IPMdHydase_lsu_aba_2.
IPR018136. Aconitase_4Fe-4S_BS.
IPR004406. Aconitase_B.
IPR015933. Aconitase_B_HEAT-like_dom.
IPR015929. Aconitase_B_swivel.
[Graphical view]
PANTHERiPTHR11670. PTHR11670. 1 hit.
PfamiPF00330. Aconitase. 1 hit.
PF06434. Aconitase_2_N. 1 hit.
PF11791. Aconitase_B_N. 1 hit.
[Graphical view]
PIRSFiPIRSF036687. AcnB. 1 hit.
SUPFAMiSSF52016. SSF52016. 1 hit.
SSF53732. SSF53732. 1 hit.
SSF74778. SSF74778. 1 hit.
TIGRFAMsiTIGR00117. acnB. 1 hit.
PROSITEiPS00450. ACONITASE_1. 1 hit.
PS01244. ACONITASE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiACNB_ECOLI
AccessioniPrimary (citable) accession number: P36683
Secondary accession number(s): P36648, P75652, Q59382
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: November 1, 1997
Last modified: November 2, 2016
This is version 156 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

AcnB is sensitive to oxidation in vivo.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.