Reviewed, UniProtKB/Swiss-Prot P13065 (PHSL_DESBA)

Names and origin

Protein names	Recommended name:     Periplasmic [NiFeSe] hydrogenase large subunit     EC=1.12.99.6 Alternative name(s):     NiFeSe hydrogenlyase large chain
Organism	Desulfovibrio baculatus (Desulfomicrobium baculatus)
Taxonomic identifier	899 [NCBI]
Taxonomic lineage	Bacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfomicrobiaceae › Desulfomicrobium

Protein attributes

Sequence length	514 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Catalytic activity	H2 + A = AH2.
Cofactor	Binds 2 irons ions. Iron 1 has 3 cyanide and carbon monoxide ligands. Iron 2 has 3 water ligands. Binds 1 nickel ion per subunit.
Subunit structure	Heterodimer of a large and a small subunit.
Subcellular location	Periplasm.
Miscellaneous	Perhaps the leader of the small subunit serves as a transport vehicle for both subunits.
Sequence similarities	Belongs to the [NiFe]/[NiFeSe] hydrogenase large subunit family.

Ontologies

Keywords
Cellular component	Periplasm
Coding sequence diversity	Selenocysteine
Ligand	Iron Metal-binding Nickel Selenium
Molecular function	Oxidoreductase
Technical term	3D-structure
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	periplasmic space Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ferredoxin hydrogenase activity Inferred from electronic annotation. Source: InterPro hydrogenase (acceptor) activity Inferred from electronic annotation. Source: EC iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW nickel ion binding Inferred from electronic annotation. Source: UniProtKB-KW selenium 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

Initiator methionine

1

1

Removed

Chain

2 – 514

513

Periplasmic [NiFeSe] hydrogenase large subunit

PRO_0000199704

Sites

Metal binding

52

1

Iron 2

Metal binding

71

1

Nickel

Metal binding

74

1

Iron 1

Metal binding

74

1

Nickel

Metal binding

445

1

Iron 2; via carbonyl oxygen

Metal binding

493

1

Nickel

Metal binding

496

1

Iron 1

Metal binding

496

1

Nickel

Metal binding

499

1

Iron 2

Amino acid modifications

Non-standard residue

493

1

Selenocysteine

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

514

Helix Strand Turn

Details...

Beta strand

14 – 19

6

Beta strand

22 – 25

4

Beta strand

27 – 34

8

Beta strand

37 – 45

9

Helix

51 – 54

4

Turn

55 – 57

3

Helix

60 – 62

3

Helix

63 – 66

4

Helix

67 – 70

4

Beta strand

72 – 74

3

Helix

75 – 90

16

Helix

96 – 120

25

Helix

123 – 125

3

Helix

145 – 148

4

Helix

152 – 184

33

Beta strand

185 – 189

5

Beta strand

191 – 194

4

Beta strand

197 – 200

4

Helix

204 – 223

20

Helix

225 – 235

11

Helix

237 – 240

4

Beta strand

249 – 251

3

Beta strand

254 – 258

5

Beta strand

264 – 266

3

Beta strand

269 – 272

4

Beta strand

275 – 277

3

Helix

281 – 283

3

Beta strand

284 – 287

4

Beta strand

296 – 299

4

Helix

303 – 305

3

Beta strand

323 – 326

4

Helix

335 – 342

8

Helix

348 – 358

11

Helix

365 – 372

8

Helix

375 – 399

25

Beta strand

414 – 424

11

Beta strand

427 – 436

10

Beta strand

439 – 447

9

Helix

449 – 452

4

Helix

464 – 469

6

Helix

481 – 489

9

Helix

494 – 498

5

Sequences

	Sequence		Length	Mass (Da)
	P13065-1 [UniParc]. Last modified February 26, 2008. Version 3. Checksum: AC920132081C1ADC	FASTA	514	56,862
	10 20 30 40 50 60 MSQAATPAAD GKVKISIDPL TRVEGHLKIE VEVKDGKVVD AKCSGGMFRG FEQILRGRDP 70 80 90 100 110 120 RDSSQIVQRI CGVCPTAHCT ASVMAQDDAF GVKVTTNGRI TRNLIFGANY LQSHILHFYH 130 140 150 160 170 180 LAALDYVKGP DVSPFVPRYA NADLLTDRIK DGAKADATNT YGLNQYLKAL EIRRICHEMV 190 200 210 220 230 240 AMFGGRMPHV QGMVVGGATE IPTADKVAEY AARFKEVQKF VIEEYLPLIY TLGSVYTDLF 250 260 270 280 290 300 ETGIGWKNVI AFGVFPEDDD YKTFLLKPGV YIDGKDEEFD SKLVKEYVGH SFFDHSAPGG 310 320 330 340 350 360 LHYSVGETNP NPDKPGAYSF VKAPRYKDKP CEVGPLARMW VQNPELSPVG QKLLKELYGI 370 380 390 400 410 420 EAKKFRDLGD KAFSIMGRHV LVAEETWLTA VAVEKWLKQV QPGAETYVKS EIPDAAEGTG 430 440 450 460 470 480 FTEAPRGALL HYLKIKDKKI ENYQIVSATL WNANPRDDMG QRGPIEEALI GVPVPDIKNP 490 500 510 VNVGRLVRSY DPULGCAVHV LHAETGEEHV VNID

References

[1]	"Cloning and sequencing of the genes encoding the large and small subunits of the periplasmic (NiFeSe) hydrogenase of Desulfovibrio baculatus." Menon N.K., Peck H.D. Jr., le Gall J., Przybyla A.E. J. Bacteriol. 169:5401-5407(1987) [PubMed: 3316183] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	Erratum Menon N.K., Pect H.D. Jr., le Gall J., Przybyla A.E. J. Bacteriol. 170:4429-4429(1988) Cited for: SEQUENCE REVISION.
[3]	"The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center." Garcin E., Vernede X., Hatchikian E.C., Volbeda A., Frey M., Fontecilla-Camps J.-C. Structure 7:557-566(1999) [PubMed: 10378275] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS), SELENOCYSTEINE AT SEC-493.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M18271 Genomic DNA. Translation: AAA23375.2.

PIR

HQDVLB. A33101.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CC1	X-ray	2.15	L	2-499	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:6125N.

Family and domain databases

InterPro

IPR001501. Ni-dep_hyd_lsu.
IPR018194. Ni-dep_hyd_lsu_Ni_BS.
[Graphical view]

Pfam

PF00374. NiFeSe_Hases. 1 hit.
[Graphical view]

PROSITE

PS00507. NI_HGENASE_L_1. 1 hit.
PS00508. NI_HGENASE_L_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

PHSL_DESBA

Accession

Primary (citable) accession number: P13065

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	February 26, 2008
Last modified:	June 16, 2009
This is version 75 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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