Reviewed, UniProtKB/Swiss-Prot P21852 (PHNL_DESVM)

Names and origin

Protein names

Recommended name:
    Periplasmic [NiFe] hydrogenase large subunit
    EC=1.12.2.1
Alternative name(s):
    NiFe hydrogenlyase large chain

Gene names

Name:	hydB
Ordered Locus Names:	DvMF_0270

Organism

Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637) [Complete proteome] [HAMAP]

Taxonomic identifier

883 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Deltaproteobacteria › Desulfovibrionales › Desulfovibrionaceae › Desulfovibrio

Protein attributes

Sequence length	567 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)

Function	Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3.
Catalytic activity	2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3.
Cofactor	Nickel. Iron.
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
Ligand	Iron Magnesium Metal-binding Nickel
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome
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	cytochrome-c3 hydrogenase activity Inferred from electronic annotation. Source: EC ferredoxin hydrogenase activity Inferred from electronic annotation. Source: InterPro iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW nickel 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 – 552

552

Periplasmic [NiFe] hydrogenase large subunit

PRO_0000013405

Propeptide

553 – 567

15

PRO_0000013406

Sites

Metal binding

62

1

Magnesium

Metal binding

81

1

Nickel

Metal binding

84

1

Iron

Metal binding

84

1

Nickel

Metal binding

498

1

Magnesium; via carbonyl oxygen

Metal binding

546

1

Nickel

Metal binding

549

1

Iron

Metal binding

549

1

Nickel

Metal binding

552

1

Magnesium; via tele nitrogen

Experimental info

Sequence conflict

180

1

S → T in AAA23370. Ref.1

Sequence conflict

514 – 515

2

KL → NV in AAA23370. Ref.1

Secondary structure

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567

Helix Strand Turn

Details...

Beta strand

23 – 29

7

Beta strand

32 – 35

4

Beta strand

37 – 44

8

Beta strand

47 – 55

9

Helix

61 – 65

5

Helix

70 – 72

3

Helix

73 – 78

6

Turn

83 – 86

4

Helix

87 – 100

14

Helix

106 – 130

25

Helix

133 – 135

3

Helix

139 – 144

6

Helix

147 – 157

11

Beta strand

158 – 160

3

Helix

164 – 179

16

Helix

184 – 186

3

Turn

190 – 193

4

Helix

202 – 230

29

Beta strand

233 – 235

3

Helix

247 – 250

4

Helix

252 – 271

20

Helix

273 – 283

11

Helix

285 – 288

4

Beta strand

296 – 298

3

Helix

309 – 311

3

Beta strand

312 – 314

3

Beta strand

317 – 320

4

Helix

332 – 334

3

Beta strand

336 – 338

3

Beta strand

344 – 347

4

Helix

352 – 354

3

Beta strand

371 – 373

3

Beta strand

375 – 380

6

Helix

387 – 396

10

Helix

400 – 413

14

Helix

417 – 420

4

Helix

423 – 453

31

Beta strand

467 – 477

11

Beta strand

480 – 489

10

Beta strand

492 – 499

8

Helix

501 – 506

6

Helix

517 – 521

5

Turn

522 – 524

3

Beta strand

530 – 532

3

Helix

534 – 542

9

Helix

547 – 551

5

Sequences

	Sequence		Length	Mass (Da)
	P21852-1 [UniParc]. Last modified April 14, 2009. Version 2. Checksum: 8BE92277C0E46FDA	FASTA	567	62,641
	10 20 30 40 50 60 MSGCRAQNAP GGIPVTPKSS YSGPIVVDPV TRIEGHLRIE VEVENGKVKN AYSSSTLFRG 70 80 90 100 110 120 LEIILKGRDP RDAQHFTQRT CGVCTYTHAL ASTRCVDNAV GVHIPKNATY IRNLVLGAQY 130 140 150 160 170 180 LHDHIVHFYH LHALDFVDVT AALKADPAKA AKVASSISPR KTTAADLKAV QDKLKTFVES 190 200 210 220 230 240 GQLGPFTNAY FLGGHPAYYL DPETNLIATA HYLEALRLQV KAARAMAVFG AKNPHTQFTV 250 260 270 280 290 300 VGGVTCYDAL TPQRIAEFEA LWKETKAFVD EVYIPDLLVV AAAYKDWTQY GGTDNFITFG 310 320 330 340 350 360 EFPKDEYDLN SRFFKPGVVF KRDFKNIKPF DKMQIEEHVR HSWYEGAEAR HPWKGQTQPK 370 380 390 400 410 420 YTDLHGDDRY SWMKAPRYMG EPMETGPLAQ VLIAYSQGHP KVKAVTDAVL AKLGVGPEAL 430 440 450 460 470 480 FSTLGRTAAR GIETAVIAEY VGVMLQEYKD NIAKGDNVIC APWEMPKQAE GVGFVNAPRG 490 500 510 520 530 540 GLSHWIRIED GKIGNFQLVV PSTWTLGPRC DKNKLSPVEA SLIGTPVADA KRPVEILRTV 550 560 HSFDPCIACG VHVIDGHTNE VHKFRIL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and sequencing of a [NiFe] hydrogenase operon from Desulfovibrio vulgaris Miyazaki F." Deckers H.M., Wilson F.R., Voordouw G. J. Gen. Microbiol. 136:2021-2028(1990) [PubMed: 2269874] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Complete sequence of Desulfovibrio vulgaris str. 'Miyazaki F'." Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Hazen T.C., Richardson P. Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis." Higuchi Y., Yagi T., Yasuoka N. Structure 5:1671-1680(1997) [PubMed: 9438867] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 19-552.
[4]	"Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution." Higuchi Y., Ogata H., Miki K., Yasuoka N., Yagi T. Structure 7:549-556(1999) [PubMed: 10378274] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M58339 Genomic DNA. Translation: AAA23370.1.
CP001197 Genomic DNA. Translation: ACL07227.1.

PIR

B45865.

RefSeq

YP_002434695.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1H2A	X-ray	1.80	L	1-567	[»]
1H2R	X-ray	1.40	L	19-552	[»]
1UBH	X-ray	1.35	L	19-552	[»]
1UBJ	X-ray	1.35	L	19-552	[»]
1UBK	X-ray	1.18	L	19-552	[»]
1UBL	X-ray	1.20	L	19-552	[»]
1UBM	X-ray	1.40	L	19-552	[»]
1UBO	X-ray	1.35	L	19-552	[»]
1UBR	X-ray	1.34	L	19-552	[»]
1UBT	X-ray	1.34	L	19-552	[»]
1UBU	X-ray	1.35	L	19-552	[»]
1WUH	X-ray	1.24	L	19-552	[»]
1WUI	X-ray	1.04	L	19-552	[»]
1WUJ	X-ray	1.40	L	19-552	[»]
1WUK	X-ray	1.10	L	19-552	[»]
1WUL	X-ray	1.50	L	19-552	[»]

ModBase

Search...

Genome annotation databases

GeneID

7172152.

GenomeReviews

Gene locus DvMF_0270 in contig CP001197_GR.

Organism-specific databases

CMR

Search...

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

PHNL_DESVM

Accession

Primary (citable) accession number: P21852
Secondary accession number(s): B8DPE0

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1991
Last sequence update:	April 14, 2009
Last modified:	June 16, 2009
This is version 68 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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