Reviewed, UniProtKB/Swiss-Prot P32131 (HEMN_ECOLI)

Names and origin

Protein names

Recommended name:
    Oxygen-independent coproporphyrinogen-III oxidase
      Short name=Coproporphyrinogenase
      Short name=Coprogen oxidase
    EC=1.3.99.22

Gene names

Name:	hemN
Synonyms:	yihJ
Ordered Locus Names:	b3867, JW3838

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	457 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Anaerobic transformation of coproporphyrinogen-III into protoporphyrinogen-IX. Ref.7
Catalytic activity	Coproporphyrinogen-III + 2 S-adenosyl-L-methionine = protoporphyrinogen-IX + 2 CO2 + 2 L-methionine + 2 5'-deoxyadenosine.
Cofactor	Binds 1 4Fe-4S cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
Pathway	Porphyrin metabolism; protoporphyrin-IX biosynthesis; protoporphyrinogen-IX from coproporphyrinogen-III (AdoMet route): step 1/1.
Subunit structure	Monomer.
Subcellular location	Cytoplasm.
Miscellaneous	The structure carries two S-adenosyl-L-methionine binding sites with only one binding to iron-cluster.
Sequence similarities	Belongs to the anaerobic coproporphyrinogen-III oxidase family.

Ontologies

Keywords
Biological process	Porphyrin biosynthesis
Cellular component	Cytoplasm
Ligand	4Fe-4S Iron Iron-sulfur Metal-binding S-adenosyl-L-methionine
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW protoporphyrinogen IX biosynthetic process from glutamate Ref.2 Inferred from genetic interaction. Source: UniProtKB
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	4 iron, 4 sulfur cluster binding Ref.6 Inferred from direct assay. Source: UniProtKB coproporphyrinogen dehydrogenase activity Ref.6 Inferred from direct assay. Source: UniProtKB coproporphyrinogen oxidase activity Inferred from electronic annotation. Source: InterPro iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 457

457

Oxygen-independent coproporphyrinogen-III oxidase

PRO_0000109941

Regions

Region

113 – 114

2

S-adenosyl-L-methionine 2 binding

Sites

Metal binding

62

1

Iron-sulfur (4Fe-4S-S-AdoMet)

Metal binding

66

1

Iron-sulfur (4Fe-4S-S-AdoMet)

Metal binding

69

1

Iron-sulfur (4Fe-4S-S-AdoMet)

Binding site

56

1

S-adenosyl-L-methionine 1

Binding site

68

1

S-adenosyl-L-methionine 2; via carbonyl oxygen

Binding site

112

1

S-adenosyl-L-methionine 1; via amide nitrogen and carbonyl oxygen

Binding site

145

1

S-adenosyl-L-methionine 1

Binding site

172

1

S-adenosyl-L-methionine 2

Binding site

184

1

S-adenosyl-L-methionine 2

Binding site

209

1

S-adenosyl-L-methionine 2

Experimental info

Mutagenesis

56

1

Y → A or L: Loss of activity. Ref.7 Ref.6

Mutagenesis

56

1

Y → F: Decreases activity by 50%. Ref.7 Ref.6

Mutagenesis

58

1

H → L: Results in loss of iron-sulfur cluster and activity. Ref.6

Mutagenesis

62

1

C → S: Results in loss of iron-sulfur cluster and activity. Ref.6

Mutagenesis

66

1

C → S: Results in loss of iron-sulfur cluster and activity. Ref.6

Mutagenesis

68

1

F → L: No effect. Ref.6

Mutagenesis

69

1

C → S: Results in loss of iron-sulfur cluster and activity. Ref.6

Mutagenesis

71

1

C → S: No effect on iron-sulfur cluster, but results in activity loss. Ref.6

Mutagenesis

111

1

G → V: Loss of activity and much less iron-sulfur cluster formed; when associated with V-113. Ref.6

Mutagenesis

113

1

G → V: Loss of activity and much less iron-sulfur cluster formed; when associated with V-111. Ref.6

Mutagenesis

145

1

E → A or I: Loss of activity. Iron content reduced by about 80%. Ref.7

Mutagenesis

310

1

F → A or L: Loss of activity. Iron content reduced by about 50%. Can cleave up to one molecule of S-adenosyl-L-methionine (in vitro). Ref.7

Mutagenesis

311

1

Q → A: Loss of activity. No change in iron content. Can cleave up to one molecule of S-adenosyl-L-methionine (in vitro). Ref.7

Mutagenesis

329

1

I → A: Loss of activity. No change in iron content. Can cleave up to one molecule of S-adenosyl-L-methionine (in vitro). Ref.7

Sequence conflict

232

1

L → V in CAA57578. Ref.2

Secondary structure

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457

Helix Strand Turn

Details...

Turn

10 – 12

3

Beta strand

25 – 27

3

Helix

29 – 31

3

Helix

38 – 45

8

Beta strand

53 – 59

7

Beta strand

61 – 64

4

Helix

80 – 96

17

Helix

97 – 100

4

Beta strand

105 – 113

9

Helix

115 – 117

3

Helix

120 – 133

14

Beta strand

136 – 146

11

Beta strand

148 – 150

3

Helix

154 – 161

8

Beta strand

166 – 172

7

Helix

176 – 182

7

Helix

188 – 200

13

Beta strand

207 – 213

7

Helix

219 – 232

14

Beta strand

235 – 241

7

Turn

246 – 248

3

Helix

250 – 254

5

Helix

257 – 259

3

Helix

263 – 279

17

Beta strand

283 – 286

4

Beta strand

289 – 291

3

Helix

296 – 303

8

Beta strand

313 – 315

3

Beta strand

320 – 325

6

Beta strand

329 – 332

4

Beta strand

335 – 339

5

Helix

343 – 353

11

Beta strand

357 – 362

6

Helix

365 – 380

16

Beta strand

381 – 384

4

Helix

385 – 391

7

Helix

396 – 399

4

Helix

401 – 412

12

Beta strand

415 – 418

4

Beta strand

420 – 425

6

Turn

427 – 429

3

Helix

430 – 432

3

Helix

433 – 438

6

Sequences

	Sequence		Length	Mass (Da)
	P32131-1 [UniParc]. Last modified November 1, 1997. Version 4. Checksum: 047EBB65D9B8F133	FASTA	457	52,729
	10 20 30 40 50 60 MSVQQIDWDL ALIQKYNYSG PRYTSYPTAL EFSEDFGEQA FLQAVARYPE RPLSLYVHIP 70 80 90 100 110 120 FCHKLCYFCG CNKIVTRQQH KADQYLDALE QEIVHRAPLF AGRHVSQLHW GGGTPTYLNK 130 140 150 160 170 180 AQISRLMKLL RENFQFNADA EISIEVDPRE IELDVLDHLR AEGFNRLSMG VQDFNKEVQR 190 200 210 220 230 240 LVNREQDEEF IFALLNHARE IGFTSTNIDL IYGLPKQTPE SFAFTLKRVA ELNPDRLSVF 250 260 270 280 290 300 NYAHLPTIFA AQRKIKDADL PSPQQKLDIL QETIAFLTQS GYQFIGMDHF ARPDDELAVA 310 320 330 340 350 360 QREGVLHRNF QGYTTQGDTD LLGMGVSAIS MIGDCYAQNQ KELKQYYQQV DEQGNALWRG 370 380 390 400 410 420 IALTRDDCIR RDVIKSLICN FRLDYAPIEK QWDLHFADYF AEDLKLLAPL AKDGLVDVDE 430 440 450 KGIQVTAKGR LLIRNICMCF DTYLRQKARM QQFSRVI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence of the downstream flanking region of the glnALG genes of Escherichia coli." Wachi M., Hamano-Takaku F., Nagano K., Kobayashi M., Yukawa H., Nagai K. Submitted (JUN-1993) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"Cloning and characterization of the Escherichia coli hemN gene encoding the oxygen-independent coproporphyrinogen III oxidase." Troup B., Hungerer C., Jahn D. J. Bacteriol. 177:3326-3331(1995) [PubMed: 7768836] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	"Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes." Plunkett G. III, Burland V., Daniels D.L., Blattner F.R. Nucleic Acids Res. 21:3391-3398(1993) [PubMed: 8346018] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"Oxygen-independent coproporphyrinogen-III oxidase HemN from Escherichia coli." Layer G., Verfuerth K., Mahlitz E., Jahn D. J. Biol. Chem. 277:34136-34142(2002) [PubMed: 12114526] [Abstract] Cited for: CHARACTERIZATION, MUTAGENESIS OF TYR-56; HIS-58; CYS-62; CYS-66; PHE-68; CYS-69; CYS-71; GLY-111 AND GLY-113.
[7]	"Radical S-adenosylmethionine enzyme coproporphyrinogen III oxidase HemN: functional features of the [4Fe-4S] cluster and the two bound S-adenosyl-L-methionines." Layer G., Grage K., Teschner T., Schuenemann V., Breckau D., Masoumi A., Jahn M., Heathcote P., Trautwein A.X., Jahn D. J. Biol. Chem. 280:29038-29046(2005) [PubMed: 15967800] [Abstract] Cited for: FUNCTIONAL FEATURES, MUTAGENESIS OF TYR-56; GLU-145; PHE-310; GLN-311 AND ILE-329.
[8]	"Crystal structure of coproporphyrinogen III oxidase reveals cofactor geometry of Radical SAM enzymes." Layer G., Moser J., Heinz D.W., Jahn D., Schubert W.-D. EMBO J. 22:6214-6224(2003) [PubMed: 14633981] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.07 ANGSTROMS), CATALYTIC MECHANISM.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

D16509 Genomic DNA. Translation: BAA03961.1.
X82073 Genomic DNA. Translation: CAA57578.1.
L19201 Genomic DNA. Translation: AAB03001.1.
U00096 Genomic DNA. Translation: AAC76864.1.
AP009048 Genomic DNA. Translation: BAE77442.1.

RefSeq

AP_003941.1.
NP_418303.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1OLT	X-ray	2.07	A	1-457	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

P32131.

Genome annotation databases

GeneID

948362.

GenomeReviews

Gene locus JW3838 in contig AP009048_GR.
Gene locus b3867 in contig U00096_GR.

KEGG

ecj:JW3838.
eco:b3867.

Organism-specific databases

EchoBASE

EB1782.

EcoGene

EG11836. hemN.

CMR

Search...

Phylogenomic databases

eggNOG

COG0635.

HOGENOM

HBG285973.

OMA

HLPSRFA.

Enzyme and pathway databases

BioCyc

EcoCyc:HEMN-MONOMER.
ECOL168927:B3867-MONOMER.
MetaCyc:HEMN-MONOMER.

Gene expression databases

Genevestigator

P32131.

Family and domain databases

InterPro

IPR006638. Elp3/MiaB/NifB.
IPR004558. HemN.
IPR010723. HemN_C.
IPR007197. Radical_SAM.
[Graphical view]

Pfam

PF06969. HemN_C. 1 hit.
PF04055. Radical_SAM. 1 hit.
[Graphical view]

SMART

SM00729. Elp3. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00538. hemN. 1 hit.

ProtoNet

Search...

Entry information

Entry name

HEMN_ECOLI

Accession

Primary (citable) accession number: P32131
Secondary accession number(s): P76772, Q2M8G4

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1993
Last sequence update:	November 1, 1997
Last modified:	February 9, 2010
This is version 93 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)