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Protein

Periplasmic [NiFe] hydrogenase small subunit

Gene

hydA

Organism
Desulfovibrio gigas
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

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

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi41Iron-sulfur 1 (4Fe-4S)1
Metal bindingi44Iron-sulfur 1 (4Fe-4S)1
Metal bindingi136Iron-sulfur 1 (4Fe-4S)1
Metal bindingi172Iron-sulfur 1 (4Fe-4S)1
Metal bindingi209Iron-sulfur 2 (4Fe-4S); via pros nitrogen1
Metal bindingi212Iron-sulfur 2 (4Fe-4S)1
Metal bindingi237Iron-sulfur 2 (4Fe-4S)1
Metal bindingi243Iron-sulfur 2 (4Fe-4S)1
Metal bindingi252Iron-sulfur 3 (3Fe-4S)1
Metal bindingi270Iron-sulfur 3 (3Fe-4S)1
Metal bindingi273Iron-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

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 gigas
Taxonomic identifieri879 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 231 PublicationAdd BLAST23
ChainiPRO_000001341624 – 288Periplasmic [NiFe] hydrogenase small subunitAdd BLAST265

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Structurei

Secondary structure

1288
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi32 – 37Combined sources6
Helixi43 – 49Combined sources7
Turni52 – 55Combined sources4
Helixi56 – 62Combined sources7
Beta strandi65 – 68Combined sources4
Turni70 – 72Combined sources3
Helixi78 – 87Combined sources10
Beta strandi90 – 101Combined sources12
Helixi103 – 105Combined sources3
Beta strandi109 – 111Combined sources3
Helixi116 – 123Combined sources8
Helixi124 – 126Combined sources3
Beta strandi127 – 133Combined sources7
Helixi134 – 139Combined sources6
Helixi142 – 144Combined sources3
Helixi155 – 159Combined sources5
Helixi160 – 162Combined sources3
Beta strandi167 – 169Combined sources3
Beta strandi171 – 173Combined sources3
Helixi176 – 188Combined sources13
Helixi201 – 204Combined sources4
Beta strandi205 – 207Combined sources3
Helixi209 – 211Combined sources3
Helixi215 – 220Combined sources6
Beta strandi225 – 229Combined sources5
Helixi230 – 233Combined sources4
Helixi239 – 241Combined sources3
Helixi245 – 247Combined sources3
Helixi252 – 255Combined sources4
Turni258 – 260Combined sources3
Turni263 – 267Combined sources5
Helixi278 – 281Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1FRVX-ray2.85A/C25-288[»]
1YQ9X-ray2.35A/B25-288[»]
2FRVX-ray2.54A/C/E/G/I/S25-288[»]
ProteinModelPortaliP12943.
SMRiP12943.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP12943.

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.
[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.

Sequencei

Sequence statusi: Complete.

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

P12943-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKFCTAVAVA MGMGPAFAPK VAEALTAKKR PSVVYLHNAE CTGCSESLLR
60 70 80 90 100
TVDPYVDELI LDVISMDYHE TLMAGAGHAV EEALHEAIKG DFVCVIEGGI
110 120 130 140 150
PMGDGGYWGK VGRRNMYDIC AEVAPKAKAV IAIGTCATYG GVQAAKPNPT
160 170 180 190 200
GTVGVNEALG KLGVKAINIA GCPPNPMNFV GTVVHLLTKG MPELDKQGRP
210 220 230 240 250
VMFFGETVHD NCPRLKHFEA GEFATSFGSP EAKKGYCLYE LGCKGPDTYN
260 270 280
NCPKQLFNQV NWPVQAGHPC IACSEPNFWD LYSPFYSA
Length:288
Mass (Da):30,816
Last modified:May 1, 1991 - v2
Checksum:i4827967DA110AE94
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti25 – 28LTAK → SEMQ AA sequence (PubMed:3322275).Curated4
Sequence conflicti47 – 48SL → LV AA sequence (PubMed:3322275).Curated2
Sequence conflicti48L → V in AAA23377 (PubMed:3322743).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M18083 Genomic DNA. Translation: AAA23377.1. Sequence problems.
PIRiA32315. HQDVSG.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M18083 Genomic DNA. Translation: AAA23377.1. Sequence problems.
PIRiA32315. HQDVSG.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1FRVX-ray2.85A/C25-288[»]
1YQ9X-ray2.35A/B25-288[»]
2FRVX-ray2.54A/C/E/G/I/S25-288[»]
ProteinModelPortaliP12943.
SMRiP12943.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP12943.

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.
[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.
ProtoNetiSearch...

Entry informationi

Entry nameiPHNS_DESGI
AccessioniPrimary (citable) accession number: P12943
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: May 1, 1991
Last modified: November 2, 2016
This is version 115 of the entry and version 2 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.