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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)DescriptionActionsGraphical viewLength
Metal bindingi50Iron-sulfur 1 (4Fe-4S)1
Metal bindingi53Iron-sulfur 1 (4Fe-4S)1
Metal bindingi158Iron-sulfur 1 (4Fe-4S)1
Metal bindingi196Iron-sulfur 1 (4Fe-4S)1
Metal bindingi240Iron-sulfur 2 (4Fe-4S); via pros nitrogen1
Metal bindingi243Iron-sulfur 2 (4Fe-4S)1
Metal bindingi263Iron-sulfur 2 (4Fe-4S)1
Metal bindingi269Iron-sulfur 2 (4Fe-4S)1
Metal bindingi278Iron-sulfur 3 (4Fe-4S)1
Metal bindingi290Iron-sulfur 3 (4Fe-4S)1
Metal bindingi296Iron-sulfur 3 (4Fe-4S)1
Metal bindingi299Iron-sulfur 3 (4Fe-4S)1

GO - Molecular functioni

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

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 32Tat-type signalPROSITE-ProRule annotation1 PublicationAdd BLAST32
ChainiPRO_000001342033 – 315Periplasmic [NiFeSe] hydrogenase small subunitAdd BLAST283

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.
STRINGi525897.Dbac_1970.

Structurei

Secondary structure

1315
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi40 – 48Combined sources9
Helixi52 – 58Combined sources7
Turni61 – 64Combined sources4
Helixi65 – 71Combined sources7
Beta strandi73 – 77Combined sources5
Turni79 – 81Combined sources3
Helixi86 – 99Combined sources14
Turni100 – 102Combined sources3
Beta strandi103 – 113Combined sources11
Helixi115 – 118Combined sources4
Beta strandi121 – 127Combined sources7
Beta strandi129 – 131Combined sources3
Beta strandi133 – 137Combined sources5
Helixi138 – 145Combined sources8
Helixi146 – 148Combined sources3
Beta strandi149 – 156Combined sources8
Helixi157 – 161Combined sources5
Helixi164 – 166Combined sources3
Helixi177 – 184Combined sources8
Beta strandi190 – 193Combined sources4
Beta strandi195 – 197Combined sources3
Helixi200 – 215Combined sources16
Turni217 – 219Combined sources3
Helixi232 – 235Combined sources4
Beta strandi236 – 238Combined sources3
Helixi240 – 242Combined sources3
Helixi246 – 250Combined sources5
Beta strandi260 – 264Combined sources5
Helixi265 – 267Combined sources3
Helixi271 – 273Combined sources3
Helixi278 – 281Combined sources4
Turni284 – 287Combined sources4
Helixi290 – 293Combined sources4
Turni302 – 305Combined sources4
Helixi306 – 308Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP13063.

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.
[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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-6126N.
MINTiMINT-96877.
STRINGi525897.Dbac_1970.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105E3S. Bacteria.
COG1740. LUCA.

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...

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: November 2, 2016
This is version 114 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

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.