Reviewed, UniProtKB/Swiss-Prot P29166 (PHF1_CLOPA)

Names and origin

Protein names	Recommended name:     Iron hydrogenase 1     EC=1.12.7.2 Alternative name(s):     [Fe] hydrogenase     Fe-only hydrogenase     CpI
Organism	Clostridium pasteurianum
Taxonomic identifier	1501 [NCBI]
Taxonomic lineage	Bacteria › Firmicutes › Clostridia › Clostridiales › Clostridiaceae › Clostridium

Protein attributes

Sequence length	574 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Catalytic activity	H2 + 2 oxidized ferredoxin = 2 reduced ferredoxin + 2 H+.
Cofactor	Binds 1 2Fe-2S cluster per subunit. Binds 4 4Fe-4S clusters per subunit. Binds 2 iron ions per subunit. Besides cysteine ligand the diiron subcluster contains non-protein ligands including 2 sulfur atoms, 1 water and 5 cyanide or carbon monoxide ligands.
Subunit structure	Monomer.
Sequence similarities	Contains 1 2Fe-2S ferredoxin-type domain. Contains 2 4Fe-4S ferredoxin-type domains.

Ontologies

Keywords
Domain	Repeat
Ligand	4Fe-4S Iron Iron-sulfur Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW electron carrier activity Inferred from electronic annotation. Source: InterPro ferredoxin hydrogenase activity Inferred from electronic annotation. Source: EC 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 – 574

574

Iron hydrogenase 1

PRO_0000199732

Regions

Domain

1 – 78

78

2Fe-2S ferredoxin-type

Domain

138 – 167

30

4Fe-4S ferredoxin-type 1

Domain

181 – 210

30

4Fe-4S ferredoxin-type 2

Sites

Metal binding

34

1

Iron-sulfur 1 (2Fe-2S) Ref.2

Metal binding

46

1

Iron-sulfur 1 (2Fe-2S) Ref.2

Metal binding

49

1

Iron-sulfur 1 (2Fe-2S) Ref.2

Metal binding

62

1

Iron-sulfur 1 (2Fe-2S) Ref.2

Metal binding

94

1

Iron-sulfur 2 (4Fe-4S); via tele nitrogen

Metal binding

98

1

Iron-sulfur 2 (4Fe-4S) Ref.2

Metal binding

101

1

Iron-sulfur 2 (4Fe-4S) Ref.2

Metal binding

107

1

Iron-sulfur 2 (4Fe-4S) Ref.2

Metal binding

147

1

Iron-sulfur 3 (4Fe-4S) Ref.2

Metal binding

150

1

Iron-sulfur 3 (4Fe-4S) Ref.2

Metal binding

153

1

Iron-sulfur 3 (4Fe-4S) Ref.2

Metal binding

157

1

Iron-sulfur 4 (4Fe-4S) Ref.2

Metal binding

190

1

Iron-sulfur 4 (4Fe-4S) Ref.2

Metal binding

193

1

Iron-sulfur 4 (4Fe-4S) Ref.2

Metal binding

196

1

Iron-sulfur 4 (4Fe-4S) Ref.2

Metal binding

200

1

Iron-sulfur 3 (4Fe-4S) Ref.2

Metal binding

300

1

Iron-sulfur 5 (4Fe-4S) Ref.2

Metal binding

355

1

Iron-sulfur 5 (4Fe-4S) Ref.2

Metal binding

499

1

Iron-sulfur 5 (4Fe-4S) Ref.2

Metal binding

503

1

Diiron subcluster

Metal binding

503

1

Iron-sulfur 5 (4Fe-4S) Ref.2

Secondary structure

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574

Helix Strand Turn

Details...

Beta strand

2 – 6

5

Beta strand

9 – 13

5

Helix

19 – 25

7

Beta strand

42 – 44

3

Beta strand

50 – 53

4

Turn

54 – 56

3

Beta strand

57 – 60

4

Helix

61 – 63

3

Beta strand

71 – 75

5

Helix

77 – 91

15

Turn

102 – 105

4

Helix

108 – 116

9

Helix

129 – 132

4

Beta strand

137 – 143

7

Helix

144 – 146

3

Helix

152 – 161

10

Beta strand

166 – 171

6

Beta strand

174 – 179

6

Helix

180 – 182

3

Helix

185 – 187

3

Helix

195 – 199

5

Beta strand

205 – 207

3

Helix

211 – 219

9

Beta strand

224 – 229

6

Helix

231 – 235

5

Helix

237 – 241

5

Helix

250 – 260

11

Beta strand

263 – 267

5

Helix

268 – 289

22

Helix

301 – 310

10

Helix

312 – 317

6

Helix

324 – 332

9

Helix

335 – 338

4

Helix

344 – 346

3

Beta strand

347 – 354

8

Helix

357 – 362

6

Beta strand

367 – 369

3

Beta strand

372 – 374

3

Beta strand

376 – 380

5

Helix

381 – 390

10

Helix

395 – 397

3

Helix

405 – 407

3

Helix

412 – 415

4

Turn

416 – 418

3

Helix

422 – 436

15

Helix

446 – 448

3

Beta strand

453 – 461

9

Beta strand

464 – 473

10

Helix

474 – 482

9

Helix

485 – 487

3

Beta strand

493 – 499

7

Helix

503 – 505

3

Helix

514 – 519

6

Helix

522 – 536

15

Helix

542 – 544

3

Helix

546 – 554

9

Helix

562 – 567

6

Sequences

	Sequence		Length	Mass (Da)
	P29166-1 [UniParc]. Last modified December 1, 1992. Version 1. Checksum: 17E28A74E23C7DEE	FASTA	574	63,828
	10 20 30 40 50 60 MKTIIINGVQ FNTDEDTTIL KFARDNNIDI SALCFLNNCN NDINKCEICT VEVEGTGLVT 70 80 90 100 110 120 ACDTLIEDGM IINTNSDAVN EKIKSRISQL LDIHEFKCGP CNRRENCEFL KLVIKYKARA 130 140 150 160 170 180 SKPFLPKDKT EYVDERSKSL TVDRTKCLLC GRCVNACGKN TETYAMKFLN KNGKTIIGAE 190 200 210 220 230 240 DEKCFDDTNC LLCGQCIIAC PVAALSEKSH MDRVKNALNA PEKHVIVAMA PSVRASIGEL 250 260 270 280 290 300 FNMGFGVDVT GKIYTALRQL GFDKIFDINF GADMTIMEEA TELVQRIENN GPFPMFTSCC 310 320 330 340 350 360 PGWVRQAENY YPELLNNLSS AKSPQQIFGT ASKTYYPSIS GLDPKNVFTV TVMPCTSKKF 370 380 390 400 410 420 EADRPQMEKD GLRDIDAVIT TRELAKMIKD AKIPFAKLED SEADPAMGEY SGAGAIFGAT 430 440 450 460 470 480 GGVMEAALRS AKDFAENAEL EDIEYKQVRG LNGIKEAEVE INNNKYNVAV INGASNLFKF 490 500 510 520 530 540 MKSGMINEKQ YHFIEVMACH GGCVNGGGQP HVNPKDLEKV DIKKVRASVL YNQDEHLSKR 550 560 570 KSHENTALVK MYQNYFGKPG EGRAHEILHF KYKK

References

[1]	"Primary structure of hydrogenase I from Clostridium pasteurianum." Meyer J., Gagnon J. Biochemistry 30:9697-9704(1991) [PubMed: 1911757] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE. Strain: ATCC 6013 / DSM 525 / NCIB 9486 / VKM B-1774 / W5.
[2]	"X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8-A resolution." Peters J.W., Lanzilotta W.N., Lemon B.J., Seefeldt L.C. Science 282:1853-1858(1998) [PubMed: 9836629] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
[3]	"Binding of exogenously added carbon monoxide at the active site of the iron-only hydrogenase (CpI) from Clostridium pasteurianum." Lemon B.J., Peters J.W. Biochemistry 38:12969-12973(1999) [PubMed: 10529166] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M81737 Genomic DNA. Translation: AAA23248.1.

PIR

HQCL1P. A40330.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1C4A	X-ray	2.40	A	1-574	[»]
1C4C	X-ray	2.40	A	1-574	[»]
1FEH	X-ray	1.80	A	1-574	[»]
3C8Y	X-ray	1.39	A	1-574	[»]

ModBase

Search...

Enzyme and pathway databases

BRENDA

1.12.7.2. 871.

Family and domain databases

InterPro

IPR006058. 2Fe2S_fd_BS.
IPR017896. 4Fe4S_Fe-S-bd.
IPR001450. 4Fe4S_Fe_S_bd_subgr.
IPR017900. 4Fe4S_Fe_S_CS.
IPR004108. Fe_hydrogenase_lsu_C.
IPR003149. Fe_hydrogenase_ssu-like.
IPR013352. Fe_hydrogenase_subset.
IPR001041. Ferredoxin.
[Graphical view]

Gene3D

G3DSA:4.10.260.20. Fe_hyd_ssu-like. 1 hit.

Pfam

PF02906. Fe_hyd_lg_C. 1 hit.
PF02256. Fe_hyd_SSU. 1 hit.
PF00111. Fer2. 1 hit.
PF00037. Fer4. 2 hits.
[Graphical view]

TIGRFAMs

TIGR02512. Fe_only_hydrog. 1 hit.

PROSITE

PS00197. 2FE2S_FER_1. False negative.
PS51085. 2FE2S_FER_2. 1 hit.
PS00198. 4FE4S_FER_1. 2 hits.
PS51379. 4FE4S_FER_2. 2 hits.
[Graphical view]

ProtoNet

Search...

Other Resources

DrugBank

DB00916. Metronidazole.

Entry information

Entry name

PHF1_CLOPA

Accession

Primary (citable) accession number: P29166

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 1, 1992
Last sequence update:	December 1, 1992
Last modified:	June 16, 2009
This is version 84 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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