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Protein

Periplasmic [NiFe] hydrogenase small subunit

Gene

hydA

Organism
Desulfovibrio fructosivorans
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in hydrogen uptake for the anaerobic reduction of sulfate to hydrogen sulfide in an electron transport chain. Cytochrome c3 is the physiological electron acceptor.

Catalytic activityi

H2 + 2 ferricytochrome c3 = 2 H+ + 2 ferrocytochrome c3.

Cofactori

Protein has several cofactor binding sites:

Redox potential

E0 is about +65 mV for the 3Fe-4S, and -340 mV for the 4Fe-4S clusters.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi67 – 671Iron-sulfur 1 (4Fe-4S)
Metal bindingi70 – 701Iron-sulfur 1 (4Fe-4S)
Metal bindingi164 – 1641Iron-sulfur 1 (4Fe-4S)
Metal bindingi197 – 1971Iron-sulfur 1 (4Fe-4S)
Metal bindingi234 – 2341Iron-sulfur 2 (4Fe-4S); via pros nitrogen
Metal bindingi237 – 2371Iron-sulfur 2 (4Fe-4S)
Metal bindingi262 – 2621Iron-sulfur 2 (4Fe-4S)
Metal bindingi268 – 2681Iron-sulfur 2 (4Fe-4S)
Metal bindingi277 – 2771Iron-sulfur 3 (3Fe-4S)
Metal bindingi295 – 2951Iron-sulfur 3 (3Fe-4S)
Metal bindingi298 – 2981Iron-sulfur 3 (3Fe-4S)

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

3Fe-4S, 4Fe-4S, Iron, Iron-sulfur, Metal-binding

Enzyme and pathway databases

BRENDAi1.12.2.1. 1906.

Names & Taxonomyi

Protein namesi
Recommended name:
Periplasmic [NiFe] hydrogenase small subunit (EC:1.12.2.1)
Alternative name(s):
NiFe hydrogenlyase small chain
Gene namesi
Name:hydA
OrganismiDesulfovibrio fructosivorans
Taxonomic identifieri878 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi238 – 2381P → C: Decreased hydrogen uptake and increased hydrogen production. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 4949Tat-type signalPROSITE-ProRule annotation1 PublicationAdd
BLAST
Chaini50 – 314265Periplasmic [NiFe] hydrogenase small subunitPRO_0000013415Add
BLAST

Post-translational modificationi

Predicted to be exported by the Tat system. The position of the signal peptide cleavage has been experimentally proven.

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.2 Publications

Protein-protein interaction databases

DIPiDIP-6172N.
MINTiMINT-1539439.
STRINGi596151.DesfrDRAFT_3948.

Structurei

Secondary structure

1
314
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi58 – 636Combined sources
Helixi69 – 746Combined sources
Turni78 – 814Combined sources
Helixi82 – 887Combined sources
Beta strandi91 – 944Combined sources
Turni96 – 983Combined sources
Helixi103 – 11412Combined sources
Beta strandi121 – 1299Combined sources
Helixi131 – 1344Combined sources
Beta strandi137 – 1393Combined sources
Helixi144 – 15411Combined sources
Beta strandi158 – 1614Combined sources
Helixi162 – 1676Combined sources
Helixi170 – 1723Combined sources
Helixi183 – 1875Combined sources
Beta strandi192 – 1943Combined sources
Beta strandi196 – 1983Combined sources
Helixi201 – 21313Combined sources
Helixi226 – 2294Combined sources
Beta strandi230 – 2323Combined sources
Helixi234 – 2363Combined sources
Helixi240 – 2445Combined sources
Beta strandi250 – 2545Combined sources
Helixi255 – 2584Combined sources
Helixi264 – 2663Combined sources
Helixi270 – 2723Combined sources
Helixi277 – 2804Combined sources
Turni283 – 2853Combined sources
Turni288 – 2925Combined sources
Helixi303 – 3064Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FRFX-ray2.70S51-314[»]
1YQWX-ray1.83A/B/C51-314[»]
1YRQX-ray2.10A/B/C/D/F/G51-313[»]
3CURX-ray2.40A/B/C51-314[»]
3CUSX-ray2.20A/B/C51-314[»]
3H3XX-ray2.70A/B/C51-314[»]
4UCQX-ray2.60A/B/C51-314[»]
4UCWX-ray2.30A/B/C51-314[»]
4UCXX-ray1.95A/B/C51-314[»]
4UE2X-ray2.02A/B/C51-314[»]
4UE6X-ray2.30A/B/C51-314[»]
4UEWX-ray2.08A/B/C51-314[»]
4UPEX-ray1.80A/B/C50-314[»]
4UPVX-ray1.52A/B50-314[»]
4UQLX-ray1.22A/B50-314[»]
4UQPX-ray1.42A/B50-314[»]
4URHX-ray1.44A/B/C50-314[»]
ProteinModelPortaliP18187.
SMRiP18187. Positions 53-314.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP18187.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4105E3S. Bacteria.
COG1740. LUCA.

Family and domain databases

Gene3Di3.40.50.700. 1 hit.
4.10.480.10. 1 hit.
InterProiIPR027394. Cytochrome-c3_hydrogenase_C.
IPR006137. NADH_UbQ_OxRdtase-like_20kDa.
IPR001821. NiFe_hydrogenase_ssu.
IPR006311. TAT_signal.
IPR019546. TAT_signal_bac_arc.
[Graphical view]
PANTHERiPTHR30013. PTHR30013. 1 hit.
PfamiPF14720. NiFe_hyd_SSU_C. 1 hit.
PF01058. Oxidored_q6. 1 hit.
PF10518. TAT_signal. 1 hit.
[Graphical view]
PIRSFiPIRSF000310. NiFe_hyd_ssu. 1 hit.
PRINTSiPR00614. NIHGNASESMLL.
TIGRFAMsiTIGR00391. hydA. 1 hit.
TIGR01409. TAT_signal_seq. 1 hit.
PROSITEiPS51318. TAT. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P18187-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNFSVGLGRD DAEKRLVQNG VSRRDFMKFC ATVAAAMGMG PAFAPKVAEA
60 70 80 90 100
LTAKHRPSVV WLHNAECTGC TEAAIRTIKP YIDALILDTI SLDYQETIMA
110 120 130 140 150
AAGEAAEAAL HQALEGKDGY YLVVEGGLPT IDGGQWGMVA GHPMIETTKK
160 170 180 190 200
AAAKAKGIIC IGTCSAYGGV QKAKPNPSQA KGVSEALGVK TINIPGCPPN
210 220 230 240 250
PINFVGAVVH VLTKGIPDLD ENGRPKLFYG ELVHDNCPRL PHFEASEFAP
260 270 280 290 300
SFDSEEAKKG FCLYELGCKG PVTYNNCPKV LFNQVNWPVQ AGHPCLGCSE
310
PDFWDTMTPF YEQG
Length:314
Mass (Da):33,621
Last modified:July 22, 2008 - v4
Checksum:i48BE00FE51D23A68
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M35333 Genomic DNA. Translation: AAA23371.2.
PIRiJQ0761. S08198.

Genome annotation databases

PATRICi41172705. VBIDesFru57976_4059.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M35333 Genomic DNA. Translation: AAA23371.2.
PIRiJQ0761. S08198.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1FRFX-ray2.70S51-314[»]
1YQWX-ray1.83A/B/C51-314[»]
1YRQX-ray2.10A/B/C/D/F/G51-313[»]
3CURX-ray2.40A/B/C51-314[»]
3CUSX-ray2.20A/B/C51-314[»]
3H3XX-ray2.70A/B/C51-314[»]
4UCQX-ray2.60A/B/C51-314[»]
4UCWX-ray2.30A/B/C51-314[»]
4UCXX-ray1.95A/B/C51-314[»]
4UE2X-ray2.02A/B/C51-314[»]
4UE6X-ray2.30A/B/C51-314[»]
4UEWX-ray2.08A/B/C51-314[»]
4UPEX-ray1.80A/B/C50-314[»]
4UPVX-ray1.52A/B50-314[»]
4UQLX-ray1.22A/B50-314[»]
4UQPX-ray1.42A/B50-314[»]
4URHX-ray1.44A/B/C50-314[»]
ProteinModelPortaliP18187.
SMRiP18187. Positions 53-314.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-6172N.
MINTiMINT-1539439.
STRINGi596151.DesfrDRAFT_3948.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

PATRICi41172705. VBIDesFru57976_4059.

Phylogenomic databases

eggNOGiENOG4105E3S. Bacteria.
COG1740. LUCA.

Enzyme and pathway databases

BRENDAi1.12.2.1. 1906.

Miscellaneous databases

EvolutionaryTraceiP18187.

Family and domain databases

Gene3Di3.40.50.700. 1 hit.
4.10.480.10. 1 hit.
InterProiIPR027394. Cytochrome-c3_hydrogenase_C.
IPR006137. NADH_UbQ_OxRdtase-like_20kDa.
IPR001821. NiFe_hydrogenase_ssu.
IPR006311. TAT_signal.
IPR019546. TAT_signal_bac_arc.
[Graphical view]
PANTHERiPTHR30013. PTHR30013. 1 hit.
PfamiPF14720. NiFe_hyd_SSU_C. 1 hit.
PF01058. Oxidored_q6. 1 hit.
PF10518. TAT_signal. 1 hit.
[Graphical view]
PIRSFiPIRSF000310. NiFe_hyd_ssu. 1 hit.
PRINTSiPR00614. NIHGNASESMLL.
TIGRFAMsiTIGR00391. hydA. 1 hit.
TIGR01409. TAT_signal_seq. 1 hit.
PROSITEiPS51318. TAT. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Cloning and sequencing of the locus encoding the large and small subunit genes of the periplasmic [NiFe]hydrogenase from Desulfovibrio fructosovorans."
    Rousset M., Dermoun Z., Matchikian C.E., Belaich J.-P.
    Gene 94:95-101(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 49200 / DSM 3604 / VKM B-1801 / JJ.
  2. "Characterization of the nickel-iron periplasmic hydrogenase from Desulfovibrio fructosovorans."
    Hatchikian C.E., Traore A.S., Fernandez V.M., Cammack R.
    Eur. J. Biochem. 187:635-643(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 50-60.
  3. "[3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis."
    Rousset M., Montet Y., Guigliarelli B., Forget N., Asso M., Bertrand P., Fontecilla-Camps J.C., Hatchikian E.C.
    Proc. Natl. Acad. Sci. U.S.A. 95:11625-11630(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 51-314 IN COMPLEX WITH HYDB AND IRON-SULFUR CLUSTERS, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF PRO-238.
  4. "Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases."
    Volbeda A., Martin L., Cavazza C., Matho M., Faber B.W., Roseboom W., Albracht S.P., Garcin E., Rousset M., Fontecilla-Camps J.C.
    J. Biol. Inorg. Chem. 10:239-249(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.83 ANGSTROMS) OF 51-314 IN COMPLEX WITH HYDB AND IRON-SULFUR CLUSTERS.

Entry informationi

Entry nameiPHNS_DESFR
AccessioniPrimary (citable) accession number: P18187
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: July 22, 2008
Last modified: July 6, 2016
This is version 126 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.