Q59334 (HEM2_CHLP8) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Delta-aminolevulinic acid dehydratase
Short name=ALAD
Short name=ALADH
EC=4.2.1.24

Alternative name(s):
Porphobilinogen synthase

Gene names

Name:	hemB
Ordered Locus Names:	Cpar_0732

Organism

Chlorobaculum parvum (strain NCIB 8327) (Chlorobium vibrioforme subsp. thiosulfatophilum (strain DSM 263 / NCIB 8327)) [Complete proteome] [HAMAP]

Taxonomic identifier

517417 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Bacteroidetes/Chlorobi group › Chlorobi › Chlorobia › Chlorobiales › Chlorobiaceae › Chlorobaculum › Chlorobaculum parvum

Protein attributes

Sequence length	328 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 activity	2 5-aminolevulinate = porphobilinogen + 2 H2O.
Enzyme regulation	Stimulated by magnesium, inhibited by zinc.
Pathway	Porphyrin-containing compound metabolism; protoporphyrin-IX biosynthesis; coproporphyrinogen-III from 5-aminolevulinate: step 1/4.
Subunit structure	Homooctamer. Ref.3
Miscellaneous	Does not seem to have a metal requirement for activity.
Sequence similarities	Belongs to the ALADH family.

Ontologies

Keywords
Biological process	Heme biosynthesis Porphyrin biosynthesis
Ligand	Magnesium Metal-binding
Molecular function	Lyase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological_process	protoporphyrinogen IX biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW porphobilinogen synthase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 328

328

Delta-aminolevulinic acid dehydratase

PRO_0000140499

Sites

Active site

200

1

Schiff-base intermediate with substrate Ref.3 Ref.4

Active site

253

1

Schiff-base intermediate with substrate Ref.3 Ref.4

Metal binding

238

1

Magnesium

Binding site

210

1

Substrate 1

Binding site

222

1

Substrate 1

Binding site

279

1

Substrate 2

Binding site

318

1

Substrate 2

Secondary structure

1

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328

Helix Strand Turn

Details...

Helix

13 – 16

4

Helix

20 – 26

7

Helix

33 – 35

3

Beta strand

36 – 47

12

Beta strand

49 – 52

4

Beta strand

55 – 62

8

Helix

63 – 75

13

Beta strand

80 – 85

6

Helix

95 – 98

4

Helix

103 – 114

12

Beta strand

118 – 124

7

Turn

127 – 129

3

Beta strand

135 – 141

7

Helix

145 – 162

18

Beta strand

165 – 169

5

Helix

176 – 186

11

Beta strand

192 – 201

10

Helix

209 – 212

4

Turn

223 – 225

3

Helix

233 – 245

13

Beta strand

248 – 254

7

Helix

256 – 258

3

Helix

259 – 269

11

Beta strand

273 – 277

5

Helix

279 – 290

12

Helix

296 – 310

15

Beta strand

313 – 317

5

Helix

320 – 327

8

Sequences

	Sequence		Length	Mass (Da)
	Q59334 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: D31B234328ABBE7B	FASTA	328	36,395
	10 20 30 40 50 60 MSQLDLLNIV HRPRRLRRTA ALRNLVQENT LTVNDLVFPL FVMPGTNAVE EVSSMPGSFR 70 80 90 100 110 120 FTIDRAVEEC KELYDLGIQG IDLFGIPEQK TEDGSEAYND NGILQQAIRA IKKAVPELCI 130 140 150 160 170 180 MTDVALDPFT PFGHDGLVKD GIILNDETVE VLQKMAVSHA EAGADFVSPS DMMDGRIGAI 190 200 210 220 230 240 REALDETDHS DVGILSYAAK YASSFYGPFR DALHSAPQFG DKSTYQMNPA NTEEAMKEVE 250 260 270 280 290 300 LDIVEGADIV MVKPGLAYLD IVWRTKERFD VPVAIYHVSG EYAMVKAAAA KGWIDEDRVM 310 320 MESLLCMKRA GADIIFTYYA KEAAKKLR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"Complete sequence of Chlorobaculum parvum NCIB 8327." US DOE Joint Genome Institute Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Zhao F., Li T., Liu Z. , Overmann J., Bryant D.A., Richardson P. Submitted (JUN-2008) to the EMBL/GenBank/DDBJ databases 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, ABSENCE OF CATALYTIC METAL COFACTOR.
[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U38348 Genomic DNA. Translation: AAC43975.1.
CP001099 Genomic DNA. Translation: ACF11151.1.

RefSeq

YP_001998351.1. NC_011027.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1W1Z	X-ray	2.60	A/B	1-328	[»]
2C1H	X-ray	2.60	A/B	1-328	[»]

ProteinModelPortal

Q59334.

SMR

Q59334. Positions 10-328.

ModBase

Search...

Protein-protein interaction databases

STRING

517417.Cpar_0732.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

ACF11151; ACF11151; Cpar_0732.

GeneID

6419660.

KEGG

cpc:Cpar_0732.

PATRIC

21364722. VBIChlPar72705_0731.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG0113.

HOGENOM

HOG000020323.

KO

K01698.

OMA

DVAIMSY.

ProtClustDB

PRK09283.

Enzyme and pathway databases

BioCyc

CPAR517417:GH95-761-MONOMER.

UniPathway

UPA00251; UER00318.

Family and domain databases

Gene3D

3.20.20.70. 1 hit.

InterPro

IPR013785. Aldolase_TIM.
IPR001731. Porphobilinogen_synth.
[Graphical view]

PANTHER

PTHR11458. PTHR11458. 1 hit.

Pfam

PF00490. ALAD. 1 hit.
[Graphical view]

PIRSF

PIRSF001415. Porphbilin_synth. 1 hit.

PRINTS

PR00144. DALDHYDRTASE.

SMART

SM01004. ALAD. 1 hit.
[Graphical view]

PROSITE

PS00169. D_ALA_DEHYDRATASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q59334.

Entry information

Entry name

HEM2_CHLP8

Accession

Primary (citable) accession number: Q59334
Secondary accession number(s): B3QMJ8

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1996
Last modified:	May 29, 2013
This is version 80 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program