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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

Manual assertion based on experiment ini

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi67Iron-sulfur 1 (4Fe-4S)1
Metal bindingi70Iron-sulfur 1 (4Fe-4S)1
Metal bindingi164Iron-sulfur 1 (4Fe-4S)1
Metal bindingi197Iron-sulfur 1 (4Fe-4S)1
Metal bindingi234Iron-sulfur 2 (4Fe-4S); via pros nitrogen1
Metal bindingi237Iron-sulfur 2 (4Fe-4S)1
Metal bindingi262Iron-sulfur 2 (4Fe-4S)1
Metal bindingi268Iron-sulfur 2 (4Fe-4S)1
Metal bindingi277Iron-sulfur 3 (3Fe-4S)1
Metal bindingi295Iron-sulfur 3 (3Fe-4S)1
Metal bindingi298Iron-sulfur 3 (3Fe-4S)1

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)DescriptionActionsGraphical viewLength
Mutagenesisi238P → C: Decreased hydrogen uptake and increased hydrogen production. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 49Tat-type signalPROSITE-ProRule annotation1 PublicationAdd BLAST49
ChainiPRO_000001341550 – 314Periplasmic [NiFe] hydrogenase small subunitAdd BLAST265

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

1314
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi58 – 63Combined sources6
Helixi69 – 74Combined sources6
Turni78 – 81Combined sources4
Helixi82 – 88Combined sources7
Beta strandi91 – 94Combined sources4
Turni96 – 98Combined sources3
Helixi103 – 114Combined sources12
Beta strandi121 – 129Combined sources9
Helixi131 – 134Combined sources4
Beta strandi137 – 139Combined sources3
Helixi144 – 154Combined sources11
Beta strandi158 – 161Combined sources4
Helixi162 – 167Combined sources6
Helixi170 – 172Combined sources3
Helixi183 – 187Combined sources5
Beta strandi192 – 194Combined sources3
Beta strandi196 – 198Combined sources3
Helixi201 – 213Combined sources13
Helixi226 – 229Combined sources4
Beta strandi230 – 232Combined sources3
Helixi234 – 236Combined sources3
Helixi240 – 244Combined sources5
Beta strandi250 – 254Combined sources5
Helixi255 – 258Combined sources4
Helixi264 – 266Combined sources3
Helixi270 – 272Combined sources3
Helixi277 – 280Combined sources4
Turni283 – 285Combined sources3
Turni288 – 292Combined sources5
Helixi303 – 306Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
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
PDB 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.
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...

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: November 2, 2016
This is version 128 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.