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P21852

- PHNL_DESVM

UniProt

P21852 - PHNL_DESVM

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Protein

Periplasmic [NiFe] hydrogenase large subunit

Gene

hydB

Organism
Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)
Status
Reviewed - 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

2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3.

Cofactori

Nickel.
Iron.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi62 – 621Magnesium
Metal bindingi81 – 811Nickel
Metal bindingi84 – 841Iron
Metal bindingi84 – 841Nickel
Metal bindingi498 – 4981Magnesium; via carbonyl oxygen
Metal bindingi546 – 5461Nickel
Metal bindingi549 – 5491Iron
Metal bindingi549 – 5491Nickel
Metal bindingi552 – 5521Magnesium; via tele nitrogen

GO - Molecular functioni

  1. cytochrome-c3 hydrogenase activity Source: UniProtKB-EC
  2. ferredoxin hydrogenase activity Source: InterPro
  3. nickel cation binding Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

Iron, Magnesium, Metal-binding, Nickel

Enzyme and pathway databases

BioCyciDVUL883:GCJ5-285-MONOMER.

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
ProteomesiUP000001361: Chromosome

Subcellular locationi

GO - Cellular componenti

  1. periplasmic space Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 552552Periplasmic [NiFe] hydrogenase large subunitPRO_0000013405Add
BLAST
Propeptidei553 – 56715PRO_0000013406Add
BLAST

Interactioni

Subunit structurei

Heterodimer of a large and a small subunit.

Protein-protein interaction databases

MINTiMINT-247638.
STRINGi883.DvMF_0270.

Structurei

Secondary structure

1
567
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi23 – 297
Beta strandi32 – 354
Beta strandi37 – 448
Beta strandi47 – 559
Helixi61 – 655
Helixi70 – 723
Helixi73 – 786
Beta strandi82 – 843
Helixi87 – 10014
Helixi106 – 13025
Helixi133 – 1353
Helixi140 – 1445
Helixi147 – 15711
Beta strandi158 – 1603
Helixi164 – 17916
Helixi184 – 1863
Turni190 – 1934
Helixi202 – 23029
Beta strandi233 – 2353
Helixi247 – 2504
Helixi252 – 27120
Helixi273 – 28311
Helixi285 – 2895
Beta strandi296 – 30510
Helixi309 – 3113
Beta strandi312 – 3209
Helixi324 – 3263
Helixi332 – 3343
Beta strandi335 – 3384
Turni340 – 3434
Beta strandi344 – 3474
Helixi352 – 3543
Beta strandi371 – 3733
Beta strandi375 – 3784
Helixi387 – 39610
Helixi400 – 41314
Helixi417 – 4204
Helixi423 – 45331
Beta strandi467 – 47711
Beta strandi480 – 48910
Beta strandi492 – 4998
Helixi501 – 5066
Helixi517 – 5226
Beta strandi530 – 5323
Helixi534 – 5429
Helixi547 – 5515

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP21852.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0374.
HOGENOMiHOG000278799.
KOiK00437.
OMAiWEMPDEA.
OrthoDBiEOG6M9DSB.

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti180 – 1801S → T in AAA23370. (PubMed:2269874)Curated
Sequence conflicti514 – 5152KL → NV in AAA23370. (PubMed:2269874)Curated

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M58339 Genomic DNA. Translation: AAA23370.1.
CP001197 Genomic DNA. Translation: ACL07227.1.
PIRiB45865.
RefSeqiWP_012611421.1. NC_011769.1.
YP_002434695.1. NC_011769.1.

Genome annotation databases

EnsemblBacteriaiACL07227; ACL07227; DvMF_0270.
GeneIDi7172152.
KEGGidvm:DvMF_0270.
PATRICi21770453. VBIDesVul86729_0281.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M58339 Genomic DNA. Translation: AAA23370.1 .
CP001197 Genomic DNA. Translation: ACL07227.1 .
PIRi B45865.
RefSeqi WP_012611421.1. NC_011769.1.
YP_002434695.1. NC_011769.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1H2A X-ray 1.80 L 1-567 [» ]
1H2R X-ray 1.40 L 19-552 [» ]
1UBH X-ray 1.35 L 19-552 [» ]
1UBJ X-ray 1.35 L 19-552 [» ]
1UBK X-ray 1.18 L 19-552 [» ]
1UBL X-ray 1.20 L 19-552 [» ]
1UBM X-ray 1.40 L 19-552 [» ]
1UBO X-ray 1.35 L 19-552 [» ]
1UBR X-ray 1.34 L 19-552 [» ]
1UBT X-ray 1.34 L 19-552 [» ]
1UBU X-ray 1.35 L 19-552 [» ]
1WUH X-ray 1.24 L 19-552 [» ]
1WUI X-ray 1.04 L 19-552 [» ]
1WUJ X-ray 1.40 L 19-552 [» ]
1WUK X-ray 1.10 L 19-552 [» ]
1WUL X-ray 1.50 L 19-552 [» ]
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

MINTi MINT-247638.
STRINGi 883.DvMF_0270.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACL07227 ; ACL07227 ; DvMF_0270 .
GeneIDi 7172152.
KEGGi dvm:DvMF_0270.
PATRICi 21770453. VBIDesVul86729_0281.

Phylogenomic databases

eggNOGi COG0374.
HOGENOMi HOG000278799.
KOi K00437.
OMAi WEMPDEA.
OrthoDBi EOG6M9DSB.

Enzyme and pathway databases

BioCyci DVUL883:GCJ5-285-MONOMER.

Miscellaneous databases

EvolutionaryTracei P21852.

Family and domain databases

Gene3Di 1.10.645.10. 1 hit.
InterProi IPR001501. Ni-dep_hyd_lsu.
IPR018194. Ni-dep_hyd_lsu_Ni_BS.
IPR029014. NiFe_Hase-like.
[Graphical view ]
Pfami PF00374. NiFeSe_Hases. 1 hit.
[Graphical view ]
SUPFAMi SSF56762. SSF56762. 1 hit.
PROSITEi PS00507. NI_HGENASE_L_1. 1 hit.
PS00508. NI_HGENASE_L_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and sequencing of a [NiFe] hydrogenase operon from Desulfovibrio vulgaris Miyazaki F."
    Deckers H.M., Wilson F.R., Voordouw G.
    J. Gen. Microbiol. 136:2021-2028(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Complete sequence of Desulfovibrio vulgaris str. 'Miyazaki F'."
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Hazen T.C., Richardson P.
    Submitted (OCT-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Miyazaki F / DSM 19637.
  3. "Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis."
    Higuchi Y., Yagi T., Yasuoka N.
    Structure 5:1671-1680(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 19-552.
  4. "Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution."
    Higuchi Y., Ogata H., Miki K., Yasuoka N., Yagi T.
    Structure 7:549-556(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS).

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: October 29, 2014
This is version 96 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

External Data

Dasty 3