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Protein

Delta-aminolevulinic acid dehydratase

Gene

hemB

Organism
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Status
Reviewed-Annotation score: Annotation score: 4 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. Required for nodule development.1 Publication

Catalytic activityi

2 5-aminolevulinate = porphobilinogen + 2 H2O.1 Publication

Cofactori

Mg2+1 Publication

Pathway: protoporphyrin-IX biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes coproporphyrinogen-III from 5-aminolevulinate.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Delta-aminolevulinic acid dehydratase (hemB)
  2. Hydroxymethylbilane synthase (hemC)
  3. no protein annotated in this organism
  4. Uroporphyrinogen decarboxylase (hemE)
This subpathway is part of the pathway protoporphyrin-IX biosynthesis, which is itself part of Porphyrin-containing compound metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes coproporphyrinogen-III from 5-aminolevulinate, the pathway protoporphyrin-IX biosynthesis and in Porphyrin-containing compound metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei221 – 2211Schiff-base intermediate with substrateBy similarity
Binding sitei231 – 2311Substrate 1By similarity
Binding sitei244 – 2441Substrate 1By similarity
Metal bindingi260 – 2601MagnesiumBy similarity
Active sitei275 – 2751Schiff-base intermediate with substrateBy similarity
Binding sitei301 – 3011Substrate 2By similarity
Binding sitei340 – 3401Substrate 2By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Heme biosynthesis, Porphyrin biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciBJAP224911:GJEJ-5074-MONOMER.
RETL1328306-WGS:GSTH-1519-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:blr5037
OrganismiBradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Taxonomic identifieri224911 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
ProteomesiUP000002526 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 353353Delta-aminolevulinic acid dehydratasePRO_0000140494Add
BLAST

Interactioni

Subunit structurei

Homooctamer.By similarity

Protein-protein interaction databases

STRINGi224911.blr5037.

Structurei

3D structure databases

ProteinModelPortaliP45622.
SMRiP45622. Positions 31-350.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the ALAD family.Curated

Phylogenomic databases

eggNOGiCOG0113.
HOGENOMiHOG000020323.
InParanoidiP45622.
KOiK01698.
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.

P45622-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAIKYGRPIE LREVSRRDGA AASPALDLAI RPRRNRKAEW ARRMVRENVL
60 70 80 90 100
TTDDLIWPLF LIDGNNKREQ IASMPGVERL SVDQAVREAE RAMKLTIPCI
110 120 130 140 150
ALFPYTDPSL RDEEGSEACN PNNLVCQAVR AIKKEFPEIG VLCDVALDPF
160 170 180 190 200
TSHGHDGLIA DGAILNDETV AVLVRQALVQ AEAGCDIIAP SDMMDGRVAA
210 220 230 240 250
IREGLDQAGL IDVQIMAYAA KYASAFYGPF RDAIGSAKTL TGDKRTYQMD
260 270 280 290 300
SANTDEALRE VELDISEGAD MVMVKPGMPY LDVVRRVKDT FAMPTFAYQV
310 320 330 340 350
SGEYAMIAAA AGNGWLDGDR AMMESLLAFK RAGADGVLSY FAPKAAEKLR

TQG
Length:353
Mass (Da):38,582
Last modified:November 1, 1995 - v1
Checksum:iF143FA4892ACF1F8
GO

Sequence cautioni

The sequence BAC50302.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L24386 Genomic DNA. Translation: AAA89067.1.
BA000040 Genomic DNA. Translation: BAC50302.1. Different initiation.
PIRiA49925.
RefSeqiNP_771677.2. NC_004463.1.

Genome annotation databases

EnsemblBacteriaiBAC50302; BAC50302; BAC50302.
GeneIDi1051848.
KEGGibja:blr5037.
PATRICi21193740. VBIBraJap65052_5115.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L24386 Genomic DNA. Translation: AAA89067.1.
BA000040 Genomic DNA. Translation: BAC50302.1. Different initiation.
PIRiA49925.
RefSeqiNP_771677.2. NC_004463.1.

3D structure databases

ProteinModelPortaliP45622.
SMRiP45622. Positions 31-350.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224911.blr5037.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC50302; BAC50302; BAC50302.
GeneIDi1051848.
KEGGibja:blr5037.
PATRICi21193740. VBIBraJap65052_5115.

Phylogenomic databases

eggNOGiCOG0113.
HOGENOMiHOG000020323.
InParanoidiP45622.
KOiK01698.
OrthoDBiEOG6VXFCB.

Enzyme and pathway databases

UniPathwayiUPA00251; UER00318.
BioCyciBJAP224911:GJEJ-5074-MONOMER.
RETL1328306-WGS:GSTH-1519-MONOMER.

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. "Bradyrhizobium japonicum delta-aminolevulinic acid dehydratase is essential for symbiosis with soybean and contains a novel metal-binding domain."
    Chauhan S., O'Brian M.R.
    J. Bacteriol. 175:7222-7227(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY, FUNCTION, COFACTOR.
    Strain: I110.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110.

Entry informationi

Entry nameiHEM2_BRADU
AccessioniPrimary (citable) accession number: P45622
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: June 24, 2015
This is version 94 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

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.