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Protein

High-molecular-weight cytochrome c

Gene

hmcA

Organism
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

HMWC (high-molecular-weight cytochrome c), ORF2, ORF3, ORF4, ORF5 and ORF6 in the HMC operon form a transmembrane protein complex that allows electron flow from the periplasmic hydrogenase to the cytoplasmic enzymes that catalyze reduction of sulfates.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi66 – 661Iron (heme 1 axial ligand)
Metal bindingi69 – 691Iron (heme 2 axial ligand)
Binding sitei80 – 801Heme 1 (covalent)
Binding sitei83 – 831Heme 1 (covalent)
Metal bindingi84 – 841Iron (heme 1 axial ligand)
Metal bindingi111 – 1111Iron (heme 3 axial ligand)
Binding sitei114 – 1141Heme 2 (covalent)
Binding sitei117 – 1171Heme 2 (covalent)
Metal bindingi118 – 1181Iron (heme 2 axial ligand)
Binding sitei135 – 1351Heme 3 (covalent)
Binding sitei138 – 1381Heme 3 (covalent)
Metal bindingi139 – 1391Iron (heme 3 axial ligand)
Metal bindingi159 – 1591Iron (heme 4 axial ligand)
Metal bindingi162 – 1621Iron (heme 6 axial ligand)
Binding sitei178 – 1781Heme 4 (covalent)
Binding sitei181 – 1811Heme 4 (covalent)
Metal bindingi182 – 1821Iron (heme 4 axial ligand)
Metal bindingi183 – 1831Iron (heme 5 axial ligand)
Binding sitei202 – 2021Heme 5 (covalent)
Binding sitei205 – 2051Heme 5 (covalent)
Metal bindingi206 – 2061Iron (heme 5 axial ligand)
Metal bindingi222 – 2221Iron (heme 7 axial ligand)
Binding sitei225 – 2251Heme 6 (covalent)
Binding sitei228 – 2281Heme 6 (covalent)
Metal bindingi229 – 2291Iron (heme 6 axial ligand)
Binding sitei244 – 2441Heme 7 (covalent)
Binding sitei247 – 2471Heme 7 (covalent)
Metal bindingi248 – 2481Iron (heme 7 axial ligand)
Metal bindingi298 – 2981Iron (heme 8 axial ligand)
Metal bindingi301 – 3011Iron (heme 10 axial ligand)
Binding sitei308 – 3081Heme 8 (covalent)
Binding sitei311 – 3111Heme 8 (covalent)
Metal bindingi312 – 3121Iron (heme 8 axial ligand)
Metal bindingi313 – 3131Iron (heme 9 axial ligand)
Binding sitei319 – 3191Heme 9 (covalent)
Binding sitei322 – 3221Heme 9 (covalent)
Metal bindingi323 – 3231Iron (heme 9 axial ligand)
Metal bindingi341 – 3411Iron (heme 12 axial ligand)
Binding sitei349 – 3491Heme 10 (covalent)
Binding sitei352 – 3521Heme 10 (covalent)
Metal bindingi353 – 3531Iron (heme 10 axial ligand)
Binding sitei362 – 3621Heme 11 (covalent)
Binding sitei365 – 3651Heme 11 (covalent)
Metal bindingi366 – 3661Iron (heme 11 axial ligand)
Binding sitei378 – 3781Heme 12 (covalent)
Binding sitei381 – 3811Heme 12 (covalent)
Metal bindingi382 – 3821Iron (heme 12 axial ligand)
Metal bindingi449 – 4491Iron (heme 13 axial ligand)
Metal bindingi470 – 4701Iron (heme 11 axial ligand)
Binding sitei477 – 4771Heme 13 (covalent)
Binding sitei480 – 4801Heme 13 (covalent)
Metal bindingi481 – 4811Iron (heme 13 axial ligand)
Metal bindingi482 – 4821Iron (heme 14 axial ligand)
Binding sitei493 – 4931Heme 14 (covalent)
Binding sitei496 – 4961Heme 14 (covalent)
Metal bindingi497 – 4971Iron (heme 14 axial ligand)
Metal bindingi516 – 5161Iron (heme 16 axial ligand)
Binding sitei519 – 5191Heme 15 (covalent)
Binding sitei522 – 5221Heme 15 (covalent)
Metal bindingi523 – 5231Iron (heme 15 axial ligand)
Binding sitei536 – 5361Heme 16 (covalent)
Binding sitei539 – 5391Heme 16 (covalent)
Metal bindingi540 – 5401Iron (heme 16 axial ligand)

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Electron transport, Transport

Keywords - Ligandi

Heme, Iron, Metal-binding

Enzyme and pathway databases

BioCyciDVUL882:GJIL-557-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
High-molecular-weight cytochrome c
Alternative name(s):
Cytochrome CC3
Gene namesi
Name:hmcA
Synonyms:hmc
Ordered Locus Names:DVU_0536
OrganismiDesulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
Taxonomic identifieri882 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaDeltaproteobacteriaDesulfovibrionalesDesulfovibrionaceaeDesulfovibrio
Proteomesi
  • UP000002194 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Periplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3131Add
BLAST
Chaini32 – 545514High-molecular-weight cytochrome cPRO_0000006593Add
BLAST

Post-translational modificationi

Binds 16 heme groups per subunit. High-spin heme 15 has single axial histidine ligand and the other hemes are low-spin bis-histidinyl coordinated.

Proteomic databases

PaxDbiP24092.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

STRINGi882.DVU0536.

Structurei

Secondary structure

1
545
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi41 – 433Combined sources
Beta strandi45 – 484Combined sources
Helixi50 – 545Combined sources
Beta strandi62 – 654Combined sources
Helixi66 – 7510Combined sources
Helixi80 – 823Combined sources
Beta strandi93 – 964Combined sources
Helixi103 – 12321Combined sources
Helixi135 – 1384Combined sources
Beta strandi144 – 1474Combined sources
Helixi156 – 1638Combined sources
Beta strandi172 – 1754Combined sources
Helixi178 – 1803Combined sources
Beta strandi184 – 1863Combined sources
Turni187 – 1904Combined sources
Beta strandi191 – 1933Combined sources
Helixi202 – 2043Combined sources
Helixi217 – 23418Combined sources
Helixi244 – 2485Combined sources
Helixi250 – 2534Combined sources
Beta strandi271 – 2755Combined sources
Beta strandi281 – 2855Combined sources
Beta strandi294 – 2974Combined sources
Helixi298 – 3047Combined sources
Turni309 – 3113Combined sources
Beta strandi312 – 3143Combined sources
Turni320 – 3223Combined sources
Helixi329 – 3313Combined sources
Helixi336 – 3416Combined sources
Beta strandi346 – 3483Combined sources
Helixi349 – 3568Combined sources
Helixi360 – 3667Combined sources
Helixi375 – 3784Combined sources
Turni379 – 3813Combined sources
Beta strandi386 – 3883Combined sources
Helixi390 – 3934Combined sources
Turni394 – 4007Combined sources
Helixi403 – 41614Combined sources
Helixi426 – 4283Combined sources
Beta strandi433 – 4353Combined sources
Beta strandi440 – 4423Combined sources
Beta strandi445 – 4473Combined sources
Helixi449 – 46012Combined sources
Helixi464 – 4696Combined sources
Turni473 – 4753Combined sources
Helixi476 – 4794Combined sources
Helixi493 – 4953Combined sources
Helixi511 – 52616Combined sources
Beta strandi538 – 5403Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GWSX-ray2.42A1-545[»]
1H29X-ray2.51A/B/C/D32-545[»]
2CVCX-ray2.00A1-545[»]
ProteinModelPortaliP24092.
SMRiP24092. Positions 41-543.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP24092.

Family & Domainsi

Keywords - Domaini

Repeat, Signal

Phylogenomic databases

eggNOGiENOG4105F1C. Bacteria.
ENOG410XRT9. LUCA.
OMAiTCRVCHH.
OrthoDBiPOG091H0RGX.

Family and domain databases

InterProiIPR002322. Cyt_c_III.
IPR020942. Cyt_c_III_dom.
IPR011346. Cyt_cc3.
IPR011031. Multihaem_cyt.
[Graphical view]
PfamiPF02085. Cytochrom_CIII. 4 hits.
[Graphical view]
PIRSFiPIRSF000026. Cytochrome_cc3. 1 hit.
PRINTSiPR00609. CYTOCHROMEC3.
SUPFAMiSSF48695. SSF48695. 1 hit.
PROSITEiPS51008. MULTIHEME_CYTC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P24092-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRNGRTLLRW AGVLAATAII GVGGFWSQGT TKALPEGPGE KRADLIEIGA
60 70 80 90 100
MERFGKLDLP KVAFRHDQHT TAVTGMGKDC AACHKSKDGK MSLKFMRLDD
110 120 130 140 150
NSAAELKEIY HANCIGCHTD LAKAGKKTGP QDGECRSCHN PKPSAASSWK
160 170 180 190 200
EIGFDKSLHY RHVASKAIKP VGDPQKNCGA CHHVYDEASK KLVWGKNKED
210 220 230 240 250
SCRACHGEKP VDKRPALDTA AHTACISCHM DVAKTKAETG PVNCAGCHAP
260 270 280 290 300
EAQAKFKVVR EVPRLDRGQP DAALILPVPG KDAPREMKGT MKPVAFDHKA
310 320 330 340 350
HEAKANDCRT CHHVRIDTCT ACHTVNGTAD SKFVQLEKAM HQPDSMRSCV
360 370 380 390 400
GCHNTRVQQP TCAGCHGFIK PTKSDAQCGV CHVAAPGFDA KQVEAGALLN
410 420 430 440 450
LKAEQRSQVA ASMLSARPQP KGTFDLNDIP EKVVIGSIAK EYQPSEFPHR
460 470 480 490 500
KIVKTLIAGI GEDKLAATFH IEKGTLCQGC HHNSPASLTP PKCASCHGKP
510 520 530 540
FDADRGDRPG LKAAYHQQCM GCHDRMKIEK PANTACVDCH KERAK
Length:545
Mass (Da):58,901
Last modified:March 1, 1992 - v1
Checksum:i70A620FCC60D070B
GO

Sequence cautioni

The sequence AAS95018 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M63807 Genomic DNA. Translation: AAA23355.1.
AE017285 Genomic DNA. Translation: AAS95018.1. Different initiation.
PIRiA39193.
RefSeqiWP_010937842.1. NC_002937.3.
YP_009759.1. NC_002937.3.

Genome annotation databases

EnsemblBacteriaiAAS95018; AAS95018; DVU_0536.
GeneIDi2795573.
KEGGidvu:DVU0536.
PATRICi32061040. VBIDesVul119526_0512.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M63807 Genomic DNA. Translation: AAA23355.1.
AE017285 Genomic DNA. Translation: AAS95018.1. Different initiation.
PIRiA39193.
RefSeqiWP_010937842.1. NC_002937.3.
YP_009759.1. NC_002937.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1GWSX-ray2.42A1-545[»]
1H29X-ray2.51A/B/C/D32-545[»]
2CVCX-ray2.00A1-545[»]
ProteinModelPortaliP24092.
SMRiP24092. Positions 41-543.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi882.DVU0536.

Proteomic databases

PaxDbiP24092.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS95018; AAS95018; DVU_0536.
GeneIDi2795573.
KEGGidvu:DVU0536.
PATRICi32061040. VBIDesVul119526_0512.

Phylogenomic databases

eggNOGiENOG4105F1C. Bacteria.
ENOG410XRT9. LUCA.
OMAiTCRVCHH.
OrthoDBiPOG091H0RGX.

Enzyme and pathway databases

BioCyciDVUL882:GJIL-557-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP24092.

Family and domain databases

InterProiIPR002322. Cyt_c_III.
IPR020942. Cyt_c_III_dom.
IPR011346. Cyt_cc3.
IPR011031. Multihaem_cyt.
[Graphical view]
PfamiPF02085. Cytochrom_CIII. 4 hits.
[Graphical view]
PIRSFiPIRSF000026. Cytochrome_cc3. 1 hit.
PRINTSiPR00609. CYTOCHROMEC3.
SUPFAMiSSF48695. SSF48695. 1 hit.
PROSITEiPS51008. MULTIHEME_CYTC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiHMWC_DESVH
AccessioniPrimary (citable) accession number: P24092
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: March 1, 1992
Last modified: September 7, 2016
This is version 119 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, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

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.