P18079 (HEM1_RHOCB) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
5-aminolevulinate synthase
EC=2.3.1.37

Alternative name(s):
5-aminolevulinic acid synthase
Delta-ALA synthase
Delta-aminolevulinate synthase

Gene names

Name:	hemA
Ordered Locus Names:	RCAP_rcc01447

Organism

Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003) [Complete proteome] [HAMAP]

Taxonomic identifier

272942 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Alphaproteobacteria › Rhodobacterales › Rhodobacteraceae › Rhodobacter › Rhodobacter capsulatus

Protein attributes

Sequence length	409 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	Succinyl-CoA + glycine = 5-aminolevulinate + CoA + CO2.
Cofactor	Pyridoxal phosphate. Ref.4
Pathway	Porphyrin metabolism; protoporphyrin-IX biosynthesis; 5-aminolevulinate from glycine: step 1/1.
Sequence similarities	Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family.

Ontologies

Keywords
Biological process	Heme biosynthesis
Ligand	Pyridoxal phosphate
Molecular function	Acyltransferase Transferase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological_process	protoporphyrinogen IX biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway
Molecular_function	5-aminolevulinate synthase activity Inferred from electronic annotation. Source: EC pyridoxal phosphate binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 409

409

5-aminolevulinate synthase

PRO_0000163828

Sites

Active site

248

1

Ref.4

Binding site

21

1

Substrate

Binding site

137

1

Substrate

Binding site

156

1

Substrate

Binding site

189

1

Pyridoxal phosphate

Binding site

217

1

Pyridoxal phosphate

Binding site

245

1

Pyridoxal phosphate

Binding site

277

1

Pyridoxal phosphate

Binding site

278

1

Pyridoxal phosphate

Binding site

365

1

Substrate

Amino acid modifications

Modified residue

248

1

N6-(pyridoxal phosphate)lysine Probable

Experimental info

Sequence conflict

128

1

V → L in CAA37857. Ref.1

Sequence conflict

128

1

V → L in CAA37393. Ref.2

Sequence conflict

402 – 409

8

Missing in CAA37857. Ref.1

Sequence conflict

402 – 409

8

Missing in CAA37393. Ref.2

Secondary structure

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409

Helix Strand Turn

Details...

Helix

3 – 16

14

Beta strand

25 – 28

4

Beta strand

35 – 39

5

Beta strand

45 – 50

6

Helix

59 – 61

3

Helix

63 – 76

14

Turn

84 – 86

3

Helix

91 – 103

13

Beta strand

107 – 113

7

Helix

115 – 129

15

Beta strand

134 – 138

5

Helix

143 – 151

9

Beta strand

156 – 159

4

Helix

164 – 173

10

Beta strand

180 – 187

8

Turn

189 – 191

3

Helix

197 – 207

11

Beta strand

210 – 214

5

Turn

216 – 221

6

Helix

229 – 233

5

Helix

236 – 238

3

Beta strand

240 – 248

9

Beta strand

255 – 259

5

Helix

261 – 270

10

Helix

272 – 275

4

Helix

282 – 295

14

Helix

298 – 321

24

Beta strand

329 – 331

3

Beta strand

333 – 336

4

Helix

340 – 354

15

Turn

363 – 365

3

Beta strand

372 – 375

4

Helix

383 – 396

14

Sequences

	Sequence		Length	Mass (Da)
	P18079 [UniParc]. Last modified May 31, 2011. Version 2. Checksum: FCC89DA6EBA8DFB3	FASTA	409	44,374
	10 20 30 40 50 60 MDYNLALDKA IQKLHDEGRY RTFIDIEREK GAFPKAQWNR PDGGKQDITV WCGNDYLGMG 70 80 90 100 110 120 QHPVVLAAMH EALEAVGAGS GGTRNISGTT AYHRRLEAEI ADLHGKEAAL VFSSAYIAND 130 140 150 160 170 180 ATLSTLRVLF PGLIIYSDSL NHASMIEGIK RNAGPKRIFR HNDVAHLREL IAADDPAAPK 190 200 210 220 230 240 LIAFESVYSM DGDFGPIKEI CDIADEFGAL TYIDEVHAVG MYGPRGAGVA ERDGLMHRID 250 260 270 280 290 300 IFNGTLAKAY GVFGGYIAAS AKMVDAVRSY APGFIFSTSL PPAIAAGAQA SIAFLKTAEG 310 320 330 340 350 360 QKLRDAQQMH AKVLKMRLKA LGMPIIDHGS HIVPVVIGDP VHTKAVSDML LSDYGVYVQP 370 380 390 400 INFPTVPRGT ERLRFTPSPV HDLKQIDGLV HAMDLLWARC ALNRAEASA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and sequencing of the hemA gene of Rhodobacter capsulatus and isolation of a delta-aminolevulinic acid-dependent mutant strain." Hornberger U., Liebetanz R., Tichy H.V., Drews G. Mol. Gen. Genet. 221:371-378(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC BAA-309 / NBRC 16581 / SB1003.
[2]	"Use of a lacZ fusion to study transcriptional regulation of the Rhodobacter capsulatus hemA gene." Wright M.S., Eckert J.J., Biel S.W., Biel A.J. FEMS Microbiol. Lett. 62:339-342(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC BAA-309 / NBRC 16581 / SB1003.
[3]	"Complete genome sequence of the photosynthetic purple nonsulfur bacterium Rhodobacter capsulatus SB 1003." Strnad H., Lapidus A., Paces J., Ulbrich P., Vlcek C., Paces V., Haselkorn R. J. Bacteriol. 192:3545-3546(2010) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC BAA-309 / NBRC 16581 / SB1003.
[4]	"Crystal structure of 5-aminolevulinate synthase, the first enzyme of heme biosynthesis, and its link to XLSA in humans." Astner I., Schulze J.O., van den Heuvel J., Jahn D., Schubert W.D., Heinz D.W. EMBO J. 24:3166-3177(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 1-401, SUBUNIT, COFACTOR-BINDING SITES, SUBSTRATE-BINDING SITES, ACTIVE SITE.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X53309 Genomic DNA. Translation: CAA37393.1.
X53864 Genomic DNA. Translation: CAA37857.1.
CP001312 Genomic DNA. Translation: ADE85192.1.

PIR

S10528.

RefSeq

YP_003577599.1. NC_014034.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2BWN	X-ray	2.10	A/B/D/E	1-401	[»]
2BWO	X-ray	2.80	A/B/D/E	1-401	[»]
2BWP	X-ray	2.70	A/B/D/E	1-401	[»]

ProteinModelPortal

P18079.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

ADE85192; ADE85192; RCAP_rcc01447.

GeneID

9004270.

KEGG

rcp:RCAP_rcc01447.

PATRIC

35502998. VBIRhoCap134200_1459.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

HOG000221020.

KO

K00643.

OMA

ICDIADE.

Enzyme and pathway databases

BioCyc

RCAP272942:GJIY-1471-MONOMER.

UniPathway

UPA00251; UER00375.

Family and domain databases

Gene3D

3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.

InterPro

IPR010961. 4pyrrol_synth_NH2levulA_synth.
IPR001917. Aminotrans_II_pyridoxalP_BS.
IPR004839. Aminotransferase_I/II.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]

Pfam

PF00155. Aminotran_1_2. 1 hit.
[Graphical view]

SUPFAM

SSF53383. PyrdxlP-dep_Trfase_major. 1 hit.

TIGRFAMs

TIGR01821. 5aminolev_synth. 1 hit.

PROSITE

PS00599. AA_TRANSFER_CLASS_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P18079.

Entry information

Entry name

HEM1_RHOCB

Accession

Primary (citable) accession number: P18079
Secondary accession number(s): D5AT85

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1990
Last sequence update:	May 31, 2011
Last modified:	May 1, 2013
This is version 98 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program