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Protein

Ribosome-binding ATPase YchF

Gene

ychF

Organism
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

ATPase that binds to both the 70S ribosome and the 50S ribosomal subunit in a nucleotide-independent manner (By similarity). Does not hydrolyze GTP.UniRule annotation1 Publication

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi16 – 161MagnesiumBy similarity
Metal bindingi36 – 361MagnesiumBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi12 – 176ATPUniRule annotation

GO - Molecular functioni

  1. ATPase activity Source: UniProtKB-HAMAP
  2. ATP binding Source: UniProtKB-HAMAP
  3. GTP binding Source: InterPro
  4. metal ion binding Source: UniProtKB-KW
  5. ribosomal large subunit binding Source: UniProtKB-HAMAP
  6. ribosome binding Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciRETL1328306-WGS:GSTH-3075-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosome-binding ATPase YchFUniRule annotation
Gene namesi
Name:ychFUniRule annotation
Synonyms:engD
Ordered Locus Names:HI_0393
OrganismiHaemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Taxonomic identifieri71421 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPasteurellalesPasteurellaceaeHaemophilus
ProteomesiUP000000579: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 363362Ribosome-binding ATPase YchFPRO_0000201678Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi71421.HI0393.

Structurei

Secondary structure

1
363
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 85Combined sources
Helixi15 – 2410Combined sources
Beta strandi41 – 455Combined sources
Helixi49 – 5810Combined sources
Beta strandi61 – 644Combined sources
Beta strandi67 – 726Combined sources
Helixi80 – 834Combined sources
Helixi84 – 863Combined sources
Helixi90 – 956Combined sources
Beta strandi98 – 1058Combined sources
Helixi121 – 15131Combined sources
Turni152 – 1543Combined sources
Helixi156 – 17318Combined sources
Helixi178 – 1803Combined sources
Helixi185 – 1917Combined sources
Helixi192 – 1943Combined sources
Beta strandi202 – 2076Combined sources
Beta strandi213 – 2153Combined sources
Helixi217 – 22812Combined sources
Beta strandi232 – 2365Combined sources
Helixi238 – 2436Combined sources
Helixi244 – 2463Combined sources
Helixi253 – 2564Combined sources
Helixi267 – 27610Combined sources
Beta strandi279 – 2857Combined sources
Beta strandi287 – 29610Combined sources
Helixi301 – 3066Combined sources
Helixi312 – 3154Combined sources
Beta strandi318 – 3225Combined sources
Helixi324 – 3296Combined sources
Helixi333 – 3386Combined sources
Beta strandi343 – 3453Combined sources
Beta strandi356 – 3616Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JALX-ray2.40A/B1-363[»]
ProteinModelPortaliP44681.
SMRiP44681. Positions 1-363.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP44681.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 256254OBG-type GAdd
BLAST

Domaini

Composed of 3 distinct structural domains: the N-terminal domain, which has a mononucleotide binding fold typical for the P-loop NTPases, followed by a pronounced alpha-helical coiled coil domain and the C-terminal domain, which may be involved in RNA binding.1 Publication

Sequence similaritiesi

Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. YchF/OLA1 subfamily.UniRule annotation

Phylogenomic databases

eggNOGiCOG0012.
KOiK06942.
OMAiYEERQMF.
OrthoDBiEOG6NSGJC.
PhylomeDBiP44681.

Family and domain databases

Gene3Di1.10.150.300. 1 hit.
3.10.20.30. 1 hit.
3.40.50.300. 2 hits.
HAMAPiMF_00944. YchF_OLA1_ATPase.
InterProiIPR004396. ATPase_YchF/OLA1.
IPR012675. Beta-grasp_dom.
IPR013029. DUF933.
IPR006073. GTP_binding_domain.
IPR027417. P-loop_NTPase.
IPR012676. TGS-like.
IPR023192. TGS-like_dom.
[Graphical view]
PfamiPF01926. MMR_HSR1. 1 hit.
PF06071. YchF-GTPase_C. 1 hit.
[Graphical view]
PIRSFiPIRSF006641. CHP00092. 1 hit.
PRINTSiPR00326. GTP1OBG.
SUPFAMiSSF52540. SSF52540. 1 hit.
SSF81271. SSF81271. 1 hit.
TIGRFAMsiTIGR00092. TIGR00092. 1 hit.
PROSITEiPS51710. G_OBG. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P44681-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGFKCGIVGL PNVGKSTLFN ALTKAGIEAA NYPFCTIEPN TGVVPMPDPR
60 70 80 90 100
LDALAEIVKP ERILPTTMEF VDIAGLVAGA SKGEGLGNKF LANIRETDAI
110 120 130 140 150
GHVVRCFEND DIVHVAGKID PLDDIDTINT ELALADLDSC ERAIQRLQKR
160 170 180 190 200
AKGGDKEAKF ELSVMEKILP VLENAGMIRS VGLDKEELQA IKSYNFLTLK
210 220 230 240 250
PTMYIANVNE DGFENNPYLD RVREIAAKEG AVVVPVCAAI ESEIAELDDE
260 270 280 290 300
EKVEFLQDLG IEEPGLNRVI RAGYALLNLQ TYFTAGVKEV RAWTVSVGAT
310 320 330 340 350
APKAAAVIHT DFEKGFIRAE VIAYEDFIQF NGENGAKEAG KWRLEGKDYI
360
VQDGDVMHFR FNV
Length:363
Mass (Da):39,751
Last modified:January 23, 2007 - v2
Checksum:i08E00CBEF7D0F65E
GO

Mass spectrometryi

Molecular mass is 40011 Da from positions 2 - 363. Determined by MALDI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L42023 Genomic DNA. Translation: AAC22052.1.
PIRiI64150.
RefSeqiNP_438555.1. NC_000907.1.

Genome annotation databases

EnsemblBacteriaiAAC22052; AAC22052; HI_0393.
GeneIDi949492.
KEGGihin:HI0393.
PATRICi20189337. VBIHaeInf48452_0412.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L42023 Genomic DNA. Translation: AAC22052.1.
PIRiI64150.
RefSeqiNP_438555.1. NC_000907.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JALX-ray2.40A/B1-363[»]
ProteinModelPortaliP44681.
SMRiP44681. Positions 1-363.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi71421.HI0393.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC22052; AAC22052; HI_0393.
GeneIDi949492.
KEGGihin:HI0393.
PATRICi20189337. VBIHaeInf48452_0412.

Phylogenomic databases

eggNOGiCOG0012.
KOiK06942.
OMAiYEERQMF.
OrthoDBiEOG6NSGJC.
PhylomeDBiP44681.

Enzyme and pathway databases

BioCyciRETL1328306-WGS:GSTH-3075-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP44681.

Family and domain databases

Gene3Di1.10.150.300. 1 hit.
3.10.20.30. 1 hit.
3.40.50.300. 2 hits.
HAMAPiMF_00944. YchF_OLA1_ATPase.
InterProiIPR004396. ATPase_YchF/OLA1.
IPR012675. Beta-grasp_dom.
IPR013029. DUF933.
IPR006073. GTP_binding_domain.
IPR027417. P-loop_NTPase.
IPR012676. TGS-like.
IPR023192. TGS-like_dom.
[Graphical view]
PfamiPF01926. MMR_HSR1. 1 hit.
PF06071. YchF-GTPase_C. 1 hit.
[Graphical view]
PIRSFiPIRSF006641. CHP00092. 1 hit.
PRINTSiPR00326. GTP1OBG.
SUPFAMiSSF52540. SSF52540. 1 hit.
SSF81271. SSF81271. 1 hit.
TIGRFAMsiTIGR00092. TIGR00092. 1 hit.
PROSITEiPS51710. G_OBG. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 51907 / DSM 11121 / KW20 / Rd.
  2. "Two-dimensional map of the proteome of Haemophilus influenzae."
    Langen H., Takacs B., Evers S., Berndt P., Lahm H.W., Wipf B., Gray C., Fountoulakis M.
    Electrophoresis 21:411-429(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: ATCC 51907 / DSM 11121 / KW20 / Rd.
  3. "Crystal structure of the YchF protein reveals binding sites for GTP and nucleic acid."
    Teplyakov A., Obmolova G., Chu S.Y., Toedt J., Eisenstein E., Howard A.J., Gilliland G.L.
    J. Bacteriol. 185:4031-4037(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS), DOMAIN.
  4. "Human OLA1 defines an ATPase subfamily in the Obg family of GTP-binding proteins."
    Koller-Eichhorn R., Marquardt T., Gail R., Wittinghofer A., Kostrewa D., Kutay U., Kambach C.
    J. Biol. Chem. 282:19928-19937(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ATPASE ACTIVITY.

Entry informationi

Entry nameiYCHF_HAEIN
AccessioniPrimary (citable) accession number: P44681
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: January 23, 2007
Last modified: March 4, 2015
This is version 116 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, Complete proteome, Reference proteome

Documents

  1. Haemophilus influenzae
    Haemophilus influenzae (strain Rd): entries and gene names
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.