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Protein

Periplasmic [NiFeSe] hydrogenase small subunit

Gene
N/A
Organism
Desulfomicrobium baculatum (Desulfovibrio baculatus)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

H2 + A = AH2.

Cofactori

[4Fe-4S] clusterNote: Binds 3 [4Fe-4S] clusters. Cluster 1 is referred to as proximal, cluster 2 as distal, cluster 3 as medial.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi50 – 501Iron-sulfur 1 (4Fe-4S)
Metal bindingi53 – 531Iron-sulfur 1 (4Fe-4S)
Metal bindingi158 – 1581Iron-sulfur 1 (4Fe-4S)
Metal bindingi196 – 1961Iron-sulfur 1 (4Fe-4S)
Metal bindingi240 – 2401Iron-sulfur 2 (4Fe-4S); via pros nitrogen
Metal bindingi243 – 2431Iron-sulfur 2 (4Fe-4S)
Metal bindingi263 – 2631Iron-sulfur 2 (4Fe-4S)
Metal bindingi269 – 2691Iron-sulfur 2 (4Fe-4S)
Metal bindingi278 – 2781Iron-sulfur 3 (4Fe-4S)
Metal bindingi290 – 2901Iron-sulfur 3 (4Fe-4S)
Metal bindingi296 – 2961Iron-sulfur 3 (4Fe-4S)
Metal bindingi299 – 2991Iron-sulfur 3 (4Fe-4S)

GO - Molecular functioni

  1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
  2. ferredoxin hydrogenase activity Source: InterPro
  3. hydrogenase (acceptor) activity Source: UniProtKB-EC
  4. metal ion binding Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

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

Names & Taxonomyi

Protein namesi
Recommended name:
Periplasmic [NiFeSe] hydrogenase small subunit (EC:1.12.99.6)
Alternative name(s):
NiFeSe hydrogenlyase small chain
OrganismiDesulfomicrobium baculatum (Desulfovibrio baculatus)
Taxonomic identifieri899 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfomicrobiaceaeDesulfomicrobium

Subcellular locationi

GO - Cellular componenti

  1. ferredoxin hydrogenase complex Source: InterPro
  2. periplasmic space Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3232Tat-type signal1 PublicationPROSITE-ProRule annotationAdd
BLAST
Chaini33 – 315283Periplasmic [NiFeSe] hydrogenase small subunitPRO_0000013420Add
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.

Protein-protein interaction databases

DIPiDIP-6126N.
MINTiMINT-96877.

Structurei

Secondary structure

1
315
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi40 – 489Combined sources
Helixi52 – 587Combined sources
Turni61 – 644Combined sources
Helixi65 – 717Combined sources
Beta strandi73 – 775Combined sources
Turni79 – 813Combined sources
Helixi86 – 9914Combined sources
Turni100 – 1023Combined sources
Beta strandi103 – 11311Combined sources
Helixi115 – 1184Combined sources
Beta strandi121 – 1277Combined sources
Beta strandi129 – 1313Combined sources
Beta strandi133 – 1375Combined sources
Helixi138 – 1458Combined sources
Helixi146 – 1483Combined sources
Beta strandi149 – 1568Combined sources
Helixi157 – 1615Combined sources
Helixi164 – 1663Combined sources
Helixi177 – 1848Combined sources
Beta strandi190 – 1934Combined sources
Beta strandi195 – 1973Combined sources
Helixi200 – 21516Combined sources
Turni217 – 2193Combined sources
Helixi232 – 2354Combined sources
Beta strandi236 – 2383Combined sources
Helixi240 – 2423Combined sources
Helixi246 – 2505Combined sources
Beta strandi260 – 2645Combined sources
Helixi265 – 2673Combined sources
Helixi271 – 2733Combined sources
Helixi278 – 2814Combined sources
Turni284 – 2874Combined sources
Helixi290 – 2934Combined sources
Turni302 – 3054Combined sources
Helixi306 – 3083Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CC1X-ray2.15S33-315[»]
4KL8X-ray1.52S/T33-315[»]
4KN9X-ray1.40S/T33-315[»]
4KO1X-ray1.55S/T33-315[»]
4KO2X-ray1.60S/T33-315[»]
4KO3X-ray1.70S/T33-315[»]
4KO4X-ray2.00S/T33-315[»]
ProteinModelPortaliP13063.
SMRiP13063. Positions 38-315.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP13063.

Family & Domainsi

Sequence similaritiesi

Keywords - Domaini

Signal

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.
[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.

P13063-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSLSRREFVK LCSAGVAGLG ISQIYHPGIV HAMTEGAKKA PVIWVQGQGC
60 70 80 90 100
TGCSVSLLNA VHPRIKEILL DVISLEFHPT VMASEGEMAL AHMYEIAEKF
110 120 130 140 150
NGNFFLLVEG AIPTAKEGRY CIVGETLDAK GHHHEVTMME LIRDLAPKSL
160 170 180 190 200
ATVAVGTCSA YGGIPAAEGN VTGSKSVRDF FADEKIEKLL VNVPGCPPHP
210 220 230 240 250
DWMVGTLVAA WSHVLNPTEH PLPELDDDGR PLLFFGDNIH ENCPYLDKYD
260 270 280 290 300
NSEFAETFTK PGCKAELGCK GPSTYADCAK RRWNNGINWC VENAVCIGCV
310
EPDFPDGKSP FYVAE
Length:315
Mass (Da):34,221
Last modified:January 1, 1990 - v1
Checksum:iA3C592F12B95ED83
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M18271 Genomic DNA. Translation: AAA23376.1.
PIRiA28380. HQDVSB.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M18271 Genomic DNA. Translation: AAA23376.1.
PIRiA28380. HQDVSB.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CC1X-ray2.15S33-315[»]
4KL8X-ray1.52S/T33-315[»]
4KN9X-ray1.40S/T33-315[»]
4KO1X-ray1.55S/T33-315[»]
4KO2X-ray1.60S/T33-315[»]
4KO3X-ray1.70S/T33-315[»]
4KO4X-ray2.00S/T33-315[»]
ProteinModelPortaliP13063.
SMRiP13063. Positions 38-315.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-6126N.
MINTiMINT-96877.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP13063.

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.
[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 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] [Europe PMC] [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. Cited for: PROTEIN SEQUENCE OF 33-67.
    Strain: DSM 1743.
  4. "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] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS).

Entry informationi

Entry nameiPHSS_DESBA
AccessioniPrimary (citable) accession number: P13063
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 1, 1990
Last modified: January 7, 2015
This is version 104 of the entry and version 1 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

External Data

Dasty 3

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 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.