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P13063

- PHSS_DESBA

UniProt

P13063 - PHSS_DESBA

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Protein
Periplasmic [NiFeSe] hydrogenase small subunit
Gene
N/A
Organism
Desulfomicrobium baculatum (Desulfovibrio baculatus)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

Functioni

Catalytic activityi

H2 + A = AH2.

Cofactori

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 Publication
Add
BLAST
Chaini33 – 315283Periplasmic [NiFeSe] hydrogenase small subunit
PRO_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

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

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]
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

MSLSRREFVK LCSAGVAGLG ISQIYHPGIV HAMTEGAKKA PVIWVQGQGC    50
TGCSVSLLNA VHPRIKEILL DVISLEFHPT VMASEGEMAL AHMYEIAEKF 100
NGNFFLLVEG AIPTAKEGRY CIVGETLDAK GHHHEVTMME LIRDLAPKSL 150
ATVAVGTCSA YGGIPAAEGN VTGSKSVRDF FADEKIEKLL VNVPGCPPHP 200
DWMVGTLVAA WSHVLNPTEH PLPELDDDGR PLLFFGDNIH ENCPYLDKYD 250
NSEFAETFTK PGCKAELGCK GPSTYADCAK RRWNNGINWC VENAVCIGCV 300
EPDFPDGKSP FYVAE 315
Length:315
Mass (Da):34,221
Last modified:January 1, 1990 - v1
Checksum:iA3C592F12B95ED83
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M18271 Genomic DNA. Translation: AAA23376.1.
PIRiA28380. HQDVSB.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M18271 Genomic DNA. Translation: AAA23376.1 .
PIRi A28380. HQDVSB.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1CC1 X-ray 2.15 S 33-315 [» ]
4KL8 X-ray 1.52 S/T 33-315 [» ]
4KN9 X-ray 1.40 S/T 33-315 [» ]
4KO1 X-ray 1.55 S/T 33-315 [» ]
4KO2 X-ray 1.60 S/T 33-315 [» ]
4KO3 X-ray 1.70 S/T 33-315 [» ]
4KO4 X-ray 2.00 S/T 33-315 [» ]
ProteinModelPortali P13063.
SMRi P13063. Positions 38-315.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-6126N.
MINTi MINT-96877.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei P13063.

Family and domain databases

Gene3Di 3.40.50.700. 1 hit.
4.10.480.10. 1 hit.
InterProi IPR027394. Cytochrome-c3_hydrogenase_C.
IPR006137. NADH_UbQ_OxRdtase-like_20kDa.
IPR001821. NiFe_hydrogenase_ssu.
IPR006311. TAT_signal.
IPR019546. TAT_signal_bac_arc.
[Graphical view ]
Pfami PF14720. NiFe_hyd_SSU_C. 1 hit.
PF01058. Oxidored_q6. 1 hit.
[Graphical view ]
PIRSFi PIRSF000310. NiFe_hyd_ssu. 1 hit.
PRINTSi PR00614. NIHGNASESMLL.
TIGRFAMsi TIGR00391. hydA. 1 hit.
TIGR01409. TAT_signal_seq. 1 hit.
PROSITEi PS51318. TAT. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: April 16, 2014
This is version 100 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

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