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Protein

Delta-aminolevulinic acid dehydratase

Gene

hemB

Organism
Chlorobaculum parvum (strain NCIB 8327) (Chlorobium vibrioforme subsp. thiosulfatophilum (strain DSM 263 / NCIB 8327))
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes an early step in the biosynthesis of tetrapyrroles. Binds two molecules of 5-aminolevulinate per subunit, each at a distinct site, and catalyzes their condensation to form porphobilinogen.

Catalytic activityi

2 5-aminolevulinate = porphobilinogen + 2 H2O.

Enzyme regulationi

Stimulated by magnesium, inhibited by zinc.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei200 – 2001Schiff-base intermediate with substrate
Binding sitei210 – 2101Substrate 1
Binding sitei222 – 2221Substrate 1
Metal bindingi238 – 2381Magnesium2 Publications
Active sitei253 – 2531Schiff-base intermediate with substrate
Binding sitei279 – 2791Substrate 2
Binding sitei318 – 3181Substrate 2

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. porphobilinogen synthase activity Source: UniProtKB-EC

GO - Biological processi

  1. protoporphyrinogen IX biosynthetic process Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Heme biosynthesis, Porphyrin biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciCPAR517417:GH95-761-MONOMER.
UniPathwayiUPA00251; UER00318.

Names & Taxonomyi

Protein namesi
Recommended name:
Delta-aminolevulinic acid dehydratase (EC:4.2.1.24)
Short name:
ALAD
Short name:
ALADH
Alternative name(s):
Porphobilinogen synthase
Gene namesi
Name:hemB
Ordered Locus Names:Cpar_0732
OrganismiChlorobaculum parvum (strain NCIB 8327) (Chlorobium vibrioforme subsp. thiosulfatophilum (strain DSM 263 / NCIB 8327))
Taxonomic identifieri517417 [NCBI]
Taxonomic lineageiBacteriaChlorobiChlorobiaChlorobialesChlorobiaceaeChlorobaculum
ProteomesiUP000008811 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 328328Delta-aminolevulinic acid dehydratasePRO_0000140499Add
BLAST

Interactioni

Subunit structurei

Homooctamer.2 Publications

Protein-protein interaction databases

STRINGi517417.Cpar_0732.

Structurei

Secondary structure

1
328
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi13 – 164Combined sources
Helixi20 – 267Combined sources
Helixi33 – 353Combined sources
Beta strandi36 – 4712Combined sources
Beta strandi49 – 524Combined sources
Beta strandi55 – 628Combined sources
Helixi63 – 7513Combined sources
Beta strandi80 – 856Combined sources
Helixi95 – 984Combined sources
Helixi103 – 11412Combined sources
Beta strandi118 – 1247Combined sources
Turni127 – 1293Combined sources
Beta strandi135 – 1417Combined sources
Helixi145 – 16218Combined sources
Beta strandi165 – 1695Combined sources
Helixi176 – 18611Combined sources
Beta strandi192 – 20110Combined sources
Helixi209 – 2124Combined sources
Turni223 – 2253Combined sources
Helixi233 – 24513Combined sources
Beta strandi248 – 2547Combined sources
Helixi256 – 2583Combined sources
Helixi259 – 26911Combined sources
Beta strandi273 – 2775Combined sources
Helixi279 – 29012Combined sources
Helixi296 – 31015Combined sources
Beta strandi313 – 3175Combined sources
Helixi320 – 3278Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1W1ZX-ray2.60A/B1-328[»]
2C1HX-ray2.60A/B1-328[»]
ProteinModelPortaliQ59334.
SMRiQ59334. Positions 10-328.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ59334.

Family & Domainsi

Sequence similaritiesi

Belongs to the ALAD family.Curated

Phylogenomic databases

eggNOGiCOG0113.
HOGENOMiHOG000020323.
KOiK01698.
OMAiSTYQMDP.
OrthoDBiEOG6VXFCB.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
InterProiIPR001731. ALAD.
IPR030656. ALAD_AS.
IPR013785. Aldolase_TIM.
[Graphical view]
PANTHERiPTHR11458. PTHR11458. 1 hit.
PfamiPF00490. ALAD. 1 hit.
[Graphical view]
PIRSFiPIRSF001415. Porphbilin_synth. 1 hit.
PRINTSiPR00144. DALDHYDRTASE.
SMARTiSM01004. ALAD. 1 hit.
[Graphical view]
PROSITEiPS00169. D_ALA_DEHYDRATASE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q59334-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQLDLLNIV HRPRRLRRTA ALRNLVQENT LTVNDLVFPL FVMPGTNAVE
60 70 80 90 100
EVSSMPGSFR FTIDRAVEEC KELYDLGIQG IDLFGIPEQK TEDGSEAYND
110 120 130 140 150
NGILQQAIRA IKKAVPELCI MTDVALDPFT PFGHDGLVKD GIILNDETVE
160 170 180 190 200
VLQKMAVSHA EAGADFVSPS DMMDGRIGAI REALDETDHS DVGILSYAAK
210 220 230 240 250
YASSFYGPFR DALHSAPQFG DKSTYQMNPA NTEEAMKEVE LDIVEGADIV
260 270 280 290 300
MVKPGLAYLD IVWRTKERFD VPVAIYHVSG EYAMVKAAAA KGWIDEDRVM
310 320
MESLLCMKRA GADIIFTYYA KEAAKKLR
Length:328
Mass (Da):36,395
Last modified:November 1, 1996 - v1
Checksum:iD31B234328ABBE7B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U38348 Genomic DNA. Translation: AAC43975.1.
CP001099 Genomic DNA. Translation: ACF11151.1.
RefSeqiYP_001998351.1. NC_011027.1.

Genome annotation databases

EnsemblBacteriaiACF11151; ACF11151; Cpar_0732.
KEGGicpc:Cpar_0732.
PATRICi21364722. VBIChlPar72705_0731.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U38348 Genomic DNA. Translation: AAC43975.1.
CP001099 Genomic DNA. Translation: ACF11151.1.
RefSeqiYP_001998351.1. NC_011027.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1W1ZX-ray2.60A/B1-328[»]
2C1HX-ray2.60A/B1-328[»]
ProteinModelPortaliQ59334.
SMRiQ59334. Positions 10-328.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi517417.Cpar_0732.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACF11151; ACF11151; Cpar_0732.
KEGGicpc:Cpar_0732.
PATRICi21364722. VBIChlPar72705_0731.

Phylogenomic databases

eggNOGiCOG0113.
HOGENOMiHOG000020323.
KOiK01698.
OMAiSTYQMDP.
OrthoDBiEOG6VXFCB.

Enzyme and pathway databases

UniPathwayiUPA00251; UER00318.
BioCyciCPAR517417:GH95-761-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ59334.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
InterProiIPR001731. ALAD.
IPR030656. ALAD_AS.
IPR013785. Aldolase_TIM.
[Graphical view]
PANTHERiPTHR11458. PTHR11458. 1 hit.
PfamiPF00490. ALAD. 1 hit.
[Graphical view]
PIRSFiPIRSF001415. Porphbilin_synth. 1 hit.
PRINTSiPR00144. DALDHYDRTASE.
SMARTiSM01004. ALAD. 1 hit.
[Graphical view]
PROSITEiPS00169. D_ALA_DEHYDRATASE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Structure and expression of the Chlorobium vibrioforme hemB gene and characterization of its encoded enzyme, porphobilinogen synthase."
    Rhie G.-E., Avissar Y.J., Beale S.I.
    J. Biol. Chem. 271:8176-8182(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: NCIB 8327.
  3. "The X-ray structure of the plant like 5-aminolaevulinic acid dehydratase from Chlorobium vibrioforme complexed with the inhibitor laevulinic acid at 2.6 A resolution."
    Coates L., Beaven G., Erskine P.T., Beale S.I., Avissar Y.J., Gill R., Mohammed F., Wood S.P., Shoolingin-Jordan P., Cooper J.B.
    J. Mol. Biol. 342:563-570(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH MAGNESIUM AND LAEVULINIC ACID, ACTIVE SITE, SUBUNIT.
  4. "Structure of Chlorobium vibrioforme 5-aminolaevulinic acid dehydratase complexed with a diacid inhibitor."
    Coates L., Beaven G., Erskine P.T., Beale S.I., Wood S.P., Shoolingin-Jordan P.M., Cooper J.B.
    Acta Crystallogr. D 61:1594-1598(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH MAGNESIUM AND 4,7-DIOXOSEBACIC ACID, ACTIVE SITE.

Entry informationi

Entry nameiHEM2_CHLP8
AccessioniPrimary (citable) accession number: Q59334
Secondary accession number(s): B3QMJ8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: April 29, 2015
This is version 91 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Does not seem to have a metal requirement for activity.1 Publication

Keywords - Technical termi

3D-structure, Complete 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

External Data

Dasty 3

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 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.