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Protein

Periplasmic [NiFe] hydrogenase large subunit

Gene

hydB

Organism
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3.

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 bindingi62Magnesium1
Metal bindingi81Nickel1
Metal bindingi84Iron1
Metal bindingi84Nickel1
Metal bindingi498Magnesium; via carbonyl oxygen1
Metal bindingi546Nickel1
Metal bindingi549Iron1
Metal bindingi549Nickel1
Metal bindingi552Magnesium; via tele nitrogen1

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

Iron, Magnesium, Metal-binding, Nickel

Names & Taxonomyi

Protein namesi
Recommended name:
Periplasmic [NiFe] hydrogenase large subunit (EC:1.12.2.1)
Alternative name(s):
NiFe hydrogenlyase large chain
Gene namesi
Name:hydB
Ordered Locus Names:DvMF_0270
OrganismiDesulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Taxonomic identifieri883 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
Proteomesi
  • UP000001361 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000134051 – 552Periplasmic [NiFe] hydrogenase large subunitAdd BLAST552
PropeptideiPRO_0000013406553 – 567Add BLAST15

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Protein-protein interaction databases

DIPiDIP-41378N.
MINTiMINT-247638.
STRINGi883.DvMF_0270.

Structurei

Secondary structure

1567
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi23 – 29Combined sources7
Beta strandi32 – 35Combined sources4
Beta strandi37 – 44Combined sources8
Beta strandi47 – 55Combined sources9
Helixi61 – 65Combined sources5
Helixi70 – 72Combined sources3
Helixi73 – 78Combined sources6
Beta strandi82 – 84Combined sources3
Helixi87 – 100Combined sources14
Helixi106 – 130Combined sources25
Helixi133 – 135Combined sources3
Helixi140 – 144Combined sources5
Helixi147 – 157Combined sources11
Beta strandi158 – 160Combined sources3
Helixi164 – 179Combined sources16
Helixi184 – 186Combined sources3
Turni190 – 193Combined sources4
Helixi202 – 230Combined sources29
Beta strandi233 – 235Combined sources3
Helixi247 – 250Combined sources4
Helixi252 – 271Combined sources20
Helixi273 – 283Combined sources11
Helixi284 – 289Combined sources6
Beta strandi296 – 305Combined sources10
Helixi309 – 311Combined sources3
Beta strandi312 – 320Combined sources9
Helixi324 – 326Combined sources3
Helixi332 – 334Combined sources3
Beta strandi335 – 338Combined sources4
Turni340 – 343Combined sources4
Beta strandi344 – 347Combined sources4
Helixi352 – 354Combined sources3
Helixi366 – 368Combined sources3
Beta strandi371 – 373Combined sources3
Beta strandi375 – 378Combined sources4
Helixi387 – 396Combined sources10
Helixi400 – 413Combined sources14
Helixi417 – 420Combined sources4
Helixi423 – 453Combined sources31
Beta strandi467 – 477Combined sources11
Beta strandi480 – 489Combined sources10
Beta strandi492 – 499Combined sources8
Helixi501 – 506Combined sources6
Helixi517 – 522Combined sources6
Beta strandi530 – 532Combined sources3
Helixi534 – 542Combined sources9
Helixi547 – 551Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1H2AX-ray1.80L1-567[»]
1H2RX-ray1.40L19-552[»]
1UBHX-ray1.35L19-552[»]
1UBJX-ray1.35L19-552[»]
1UBKX-ray1.18L19-552[»]
1UBLX-ray1.20L19-552[»]
1UBMX-ray1.40L19-552[»]
1UBOX-ray1.35L19-552[»]
1UBRX-ray1.34L19-552[»]
1UBTX-ray1.34L19-552[»]
1UBUX-ray1.35L19-552[»]
1WUHX-ray1.24L19-552[»]
1WUIX-ray1.04L19-552[»]
1WUJX-ray1.40L19-552[»]
1WUKX-ray1.10L19-552[»]
1WULX-ray1.50L19-552[»]
4U9HX-ray0.89L20-552[»]
4U9IX-ray1.06L20-552[»]
SMRiP21852.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP21852.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105DPX. Bacteria.
COG0374. LUCA.
HOGENOMiHOG000278799.
KOiK00437.
OMAiGWHNAPR.
OrthoDBiPOG091H05OW.

Family and domain databases

Gene3Di1.10.645.10. 1 hit.
InterProiIPR001501. Ni-dep_hyd_lsu.
IPR018194. Ni-dep_hyd_lsu_Ni_BS.
IPR029014. NiFe_Hase-like.
[Graphical view]
PfamiPF00374. NiFeSe_Hases. 1 hit.
[Graphical view]
SUPFAMiSSF56762. SSF56762. 1 hit.
PROSITEiPS00507. NI_HGENASE_L_1. 1 hit.
PS00508. NI_HGENASE_L_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P21852-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGCRAQNAP GGIPVTPKSS YSGPIVVDPV TRIEGHLRIE VEVENGKVKN
60 70 80 90 100
AYSSSTLFRG LEIILKGRDP RDAQHFTQRT CGVCTYTHAL ASTRCVDNAV
110 120 130 140 150
GVHIPKNATY IRNLVLGAQY LHDHIVHFYH LHALDFVDVT AALKADPAKA
160 170 180 190 200
AKVASSISPR KTTAADLKAV QDKLKTFVES GQLGPFTNAY FLGGHPAYYL
210 220 230 240 250
DPETNLIATA HYLEALRLQV KAARAMAVFG AKNPHTQFTV VGGVTCYDAL
260 270 280 290 300
TPQRIAEFEA LWKETKAFVD EVYIPDLLVV AAAYKDWTQY GGTDNFITFG
310 320 330 340 350
EFPKDEYDLN SRFFKPGVVF KRDFKNIKPF DKMQIEEHVR HSWYEGAEAR
360 370 380 390 400
HPWKGQTQPK YTDLHGDDRY SWMKAPRYMG EPMETGPLAQ VLIAYSQGHP
410 420 430 440 450
KVKAVTDAVL AKLGVGPEAL FSTLGRTAAR GIETAVIAEY VGVMLQEYKD
460 470 480 490 500
NIAKGDNVIC APWEMPKQAE GVGFVNAPRG GLSHWIRIED GKIGNFQLVV
510 520 530 540 550
PSTWTLGPRC DKNKLSPVEA SLIGTPVADA KRPVEILRTV HSFDPCIACG
560
VHVIDGHTNE VHKFRIL
Length:567
Mass (Da):62,641
Last modified:April 14, 2009 - v2
Checksum:i8BE92277C0E46FDA
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti180S → T in AAA23370 (PubMed:2269874).Curated1
Sequence conflicti514 – 515KL → NV in AAA23370 (PubMed:2269874).Curated2

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M58339 Genomic DNA. Translation: AAA23370.1.
CP001197 Genomic DNA. Translation: ACL07227.1.
PIRiB45865.
RefSeqiWP_012611421.1. NC_011769.1.

Genome annotation databases

EnsemblBacteriaiACL07227; ACL07227; DvMF_0270.
KEGGidvm:DvMF_0270.
PATRICi21770453. VBIDesVul86729_0281.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M58339 Genomic DNA. Translation: AAA23370.1.
CP001197 Genomic DNA. Translation: ACL07227.1.
PIRiB45865.
RefSeqiWP_012611421.1. NC_011769.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1H2AX-ray1.80L1-567[»]
1H2RX-ray1.40L19-552[»]
1UBHX-ray1.35L19-552[»]
1UBJX-ray1.35L19-552[»]
1UBKX-ray1.18L19-552[»]
1UBLX-ray1.20L19-552[»]
1UBMX-ray1.40L19-552[»]
1UBOX-ray1.35L19-552[»]
1UBRX-ray1.34L19-552[»]
1UBTX-ray1.34L19-552[»]
1UBUX-ray1.35L19-552[»]
1WUHX-ray1.24L19-552[»]
1WUIX-ray1.04L19-552[»]
1WUJX-ray1.40L19-552[»]
1WUKX-ray1.10L19-552[»]
1WULX-ray1.50L19-552[»]
4U9HX-ray0.89L20-552[»]
4U9IX-ray1.06L20-552[»]
SMRiP21852.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-41378N.
MINTiMINT-247638.
STRINGi883.DvMF_0270.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACL07227; ACL07227; DvMF_0270.
KEGGidvm:DvMF_0270.
PATRICi21770453. VBIDesVul86729_0281.

Phylogenomic databases

eggNOGiENOG4105DPX. Bacteria.
COG0374. LUCA.
HOGENOMiHOG000278799.
KOiK00437.
OMAiGWHNAPR.
OrthoDBiPOG091H05OW.

Miscellaneous databases

EvolutionaryTraceiP21852.

Family and domain databases

Gene3Di1.10.645.10. 1 hit.
InterProiIPR001501. Ni-dep_hyd_lsu.
IPR018194. Ni-dep_hyd_lsu_Ni_BS.
IPR029014. NiFe_Hase-like.
[Graphical view]
PfamiPF00374. NiFeSe_Hases. 1 hit.
[Graphical view]
SUPFAMiSSF56762. SSF56762. 1 hit.
PROSITEiPS00507. NI_HGENASE_L_1. 1 hit.
PS00508. NI_HGENASE_L_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPHNL_DESVM
AccessioniPrimary (citable) accession number: P21852
Secondary accession number(s): B8DPE0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1991
Last sequence update: April 14, 2009
Last modified: November 2, 2016
This is version 111 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Perhaps the leader of the small subunit serves as a transport vehicle for both subunits.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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.