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Protein

Delta-aminolevulinic acid dehydratase

Gene

hemB

Organism
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
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 (By similarity).By similarity

Catalytic activityi

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

Cofactori

Mg2+2 Publications

Enzyme regulationi

Stimulated by magnesium ions.

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei205 – 2051Schiff-base intermediate with substrate2 Publications
Binding sitei215 – 2151Substrate 12 Publications
Binding sitei229 – 2291Substrate 12 Publications
Metal bindingi245 – 2451Magnesium2 Publications
Active sitei260 – 2601Schiff-base intermediate with substrate2 Publications
Binding sitei286 – 2861Substrate 22 Publications
Binding sitei324 – 3241Substrate 22 Publications

GO - Molecular functioni

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

GO - Biological processi

  1. porphyrin-containing compound biosynthetic process Source: PseudoCAP
  2. 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

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:PA5243
OrganismiPseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Taxonomic identifieri208964 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
ProteomesiUP000002438: Chromosome

Organism-specific databases

PseudoCAPiPA5243.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 337337Delta-aminolevulinic acid dehydratasePRO_0000140507Add
BLAST

Interactioni

Subunit structurei

Homooctamer; formed by oligomerization of dimers.3 Publications

Protein-protein interaction databases

STRINGi208964.PA5243.

Structurei

Secondary structure

1
337
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni10 – 123Combined sources
Turni15 – 195Combined sources
Helixi22 – 287Combined sources
Helixi35 – 373Combined sources
Beta strandi38 – 4912Combined sources
Beta strandi51 – 533Combined sources
Beta strandi61 – 644Combined sources
Helixi65 – 7713Combined sources
Beta strandi82 – 876Combined sources
Helixi91 – 933Combined sources
Beta strandi95 – 973Combined sources
Helixi99 – 1024Combined sources
Helixi107 – 11812Combined sources
Beta strandi122 – 1287Combined sources
Turni131 – 1333Combined sources
Beta strandi134 – 1363Combined sources
Helixi150 – 16617Combined sources
Beta strandi170 – 1745Combined sources
Helixi181 – 19111Combined sources
Beta strandi198 – 2069Combined sources
Helixi209 – 2113Combined sources
Helixi212 – 2165Combined sources
Helixi221 – 2244Combined sources
Helixi229 – 2313Combined sources
Beta strandi232 – 2343Combined sources
Helixi240 – 25112Combined sources
Beta strandi255 – 2617Combined sources
Helixi263 – 2653Combined sources
Helixi266 – 27611Combined sources
Beta strandi280 – 2845Combined sources
Helixi286 – 29712Combined sources
Helixi305 – 31612Combined sources
Beta strandi319 – 3235Combined sources
Helixi326 – 3349Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1B4KX-ray1.67A/B1-337[»]
1GZGX-ray1.66A/B1-337[»]
1W54X-ray2.20A/B1-337[»]
1W56X-ray1.70A/B1-337[»]
1W5MX-ray1.60A/B1-337[»]
1W5NX-ray1.65A/B1-337[»]
1W5OX-ray1.85A/B1-337[»]
1W5PX-ray1.55A/B1-337[»]
1W5QX-ray1.40A/B1-337[»]
2C13X-ray2.15A/B1-337[»]
2C14X-ray1.90A/B1-337[»]
2C15X-ray1.48A/B1-337[»]
2C16X-ray2.02A/B1-337[»]
2C18X-ray1.93A/B1-337[»]
2C19X-ray2.05A/B1-337[»]
2WOQX-ray1.75A1-337[»]
ProteinModelPortaliQ59643.
SMRiQ59643. Positions 10-335.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ59643.

Family & Domainsi

Sequence similaritiesi

Belongs to the ALAD family.Curated

Phylogenomic databases

eggNOGiCOG0113.
HOGENOMiHOG000020323.
InParanoidiQ59643.
KOiK01698.
OMAiSTYQMDP.
OrthoDBiEOG6VXFCB.
PhylomeDBiQ59643.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR001731. Porphobilinogen_synth.
[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.

Q59643-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSFTPANRAY PYTRLRRNRR DDFSRRLVRE NVLTVDDLIL PVFVLDGVNQ
60 70 80 90 100
RESIPSMPGV ERLSIDQLLI EAEEWVALGI PALALFPVTP VEKKSLDAAE
110 120 130 140 150
AYNPEGIAQR ATRALRERFP ELGIITDVAL DPFTTHGQDG ILDDDGYVLN
160 170 180 190 200
DVSIDVLVRQ ALSHAEAGAQ VVAPSDMMDG RIGAIREALE SAGHTNVRIM
210 220 230 240 250
AYSAKYASAY YGPFRDAVGS ASNLGKGNKA TYQMDPANSD EALHEVAADL
260 270 280 290 300
AEGADMVMVK PGMPYLDIVR RVKDEFRAPT FVYQVSGEYA MHMGAIQNGW
310 320 330
LAESVILESL TAFKRAGADG ILTYFAKQAA EQLRRGR
Length:337
Mass (Da):37,037
Last modified:November 1, 1996 - v1
Checksum:i7D650C49795D542C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X91820 Genomic DNA. Translation: CAA62930.1.
AE004091 Genomic DNA. Translation: AAG08628.1.
PIRiS60577.
RefSeqiNP_253930.1. NC_002516.2.

Genome annotation databases

EnsemblBacteriaiAAG08628; AAG08628; PA5243.
GeneIDi879701.
KEGGipae:PA5243.
PATRICi19845337. VBIPseAer58763_5495.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X91820 Genomic DNA. Translation: CAA62930.1.
AE004091 Genomic DNA. Translation: AAG08628.1.
PIRiS60577.
RefSeqiNP_253930.1. NC_002516.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1B4KX-ray1.67A/B1-337[»]
1GZGX-ray1.66A/B1-337[»]
1W54X-ray2.20A/B1-337[»]
1W56X-ray1.70A/B1-337[»]
1W5MX-ray1.60A/B1-337[»]
1W5NX-ray1.65A/B1-337[»]
1W5OX-ray1.85A/B1-337[»]
1W5PX-ray1.55A/B1-337[»]
1W5QX-ray1.40A/B1-337[»]
2C13X-ray2.15A/B1-337[»]
2C14X-ray1.90A/B1-337[»]
2C15X-ray1.48A/B1-337[»]
2C16X-ray2.02A/B1-337[»]
2C18X-ray1.93A/B1-337[»]
2C19X-ray2.05A/B1-337[»]
2WOQX-ray1.75A1-337[»]
ProteinModelPortaliQ59643.
SMRiQ59643. Positions 10-335.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi208964.PA5243.

Protocols and materials databases

DNASUi879701.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAG08628; AAG08628; PA5243.
GeneIDi879701.
KEGGipae:PA5243.
PATRICi19845337. VBIPseAer58763_5495.

Organism-specific databases

PseudoCAPiPA5243.

Phylogenomic databases

eggNOGiCOG0113.
HOGENOMiHOG000020323.
InParanoidiQ59643.
KOiK01698.
OMAiSTYQMDP.
OrthoDBiEOG6VXFCB.
PhylomeDBiQ59643.

Enzyme and pathway databases

UniPathwayiUPA00251; UER00318.

Miscellaneous databases

EvolutionaryTraceiQ59643.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR001731. Porphobilinogen_synth.
[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. "Cloning, mapping and functional characterization of the hemB gene of Pseudomonas aeruginosa, which encodes a magnesium-dependent 5-aminolevulinic acid dehydratase."
    Frankenberg N., Kittel T., Hungerer C., Roemling U., Jahn D.
    Mol. Gen. Genet. 257:485-489(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228.
  3. "High resolution crystal structure of a Mg(2+)-dependent porphobilinogen synthase."
    Frankenberg N., Erskine P.T., Cooper J.B., Shoolingin-Jordan P.M., Jahn D., Heinz D.W.
    J. Mol. Biol. 289:591-602(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.67 ANGSTROMS) IN COMPLEX WITH LEVULINIC ACID AND MAGNESIUM, SUBUNIT.
  4. "Structure of porphobilinogen synthase from Pseudomonas aeruginosa in complex with 5-fluorolevulinic acid suggests a double Schiff base mechanism."
    Frere F., Schubert W.-D., Stauffer F., Frankenberg N., Neier R., Jahn D., Heinz D.W.
    J. Mol. Biol. 320:237-247(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.66 ANGSTROMS) OF MUTANT ASN-139 IN COMPLEX WITH 5-FLUOROLEVULINIC ACID AND MAGNESIUM, COFACTOR, ACTIVE SITE.
  5. "Probing the active site of Pseudomonas aeruginosa porphobilinogen synthase using newly developed inhibitors."
    Frere F., Nentwich M., Gacond S., Heinz D.W., Neier R., Frankenberg-Dinkel N.
    Biochemistry 45:8243-8253(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.48 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM; 5-HYDROXYLEVULINIC ACID AND OTHER INHIBITORS, CATALYTIC ACTIVITY, COFACTOR, ACTIVE SITE.
  6. "Structure of the heme biosynthetic Pseudomonas aeruginosa porphobilinogen synthase in complex with the antibiotic alaremycin."
    Heinemann I.U., Schulz C., Schubert W.D., Heinz D.W., Wang Y.G., Kobayashi Y., Awa Y., Wachi M., Jahn D., Jahn M.
    Antimicrob. Agents Chemother. 54:267-272(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) IN COMPLEX WITH ALAREMYCIN.

Entry informationi

Entry nameiHEM2_PSEAE
AccessioniPrimary (citable) accession number: Q59643
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: February 4, 2015
This is version 114 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

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.