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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)DescriptionActionsGraphical viewLength
Metal bindingi16MagnesiumBy similarity1
Metal bindingi36MagnesiumBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi12 – 17ATPUniRule annotation6

GO - Molecular functioni

Complete GO annotation...

Keywords - Ligandi

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

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
Proteomesi
  • UP000000579 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00002016782 – 363Ribosome-binding ATPase YchFAdd BLAST362

Interactioni

Protein-protein interaction databases

STRINGi71421.HI0393.

Structurei

Secondary structure

1363
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 8Combined sources5
Helixi15 – 24Combined sources10
Beta strandi41 – 45Combined sources5
Helixi49 – 58Combined sources10
Beta strandi61 – 64Combined sources4
Beta strandi67 – 72Combined sources6
Helixi80 – 83Combined sources4
Helixi84 – 86Combined sources3
Helixi90 – 95Combined sources6
Beta strandi98 – 105Combined sources8
Helixi121 – 151Combined sources31
Turni152 – 154Combined sources3
Helixi156 – 173Combined sources18
Helixi178 – 180Combined sources3
Helixi185 – 191Combined sources7
Helixi192 – 194Combined sources3
Beta strandi202 – 207Combined sources6
Beta strandi213 – 215Combined sources3
Helixi217 – 228Combined sources12
Beta strandi232 – 236Combined sources5
Helixi238 – 243Combined sources6
Helixi244 – 246Combined sources3
Helixi253 – 256Combined sources4
Helixi267 – 276Combined sources10
Beta strandi279 – 285Combined sources7
Beta strandi287 – 296Combined sources10
Helixi301 – 306Combined sources6
Helixi312 – 315Combined sources4
Beta strandi318 – 322Combined sources5
Helixi324 – 329Combined sources6
Helixi333 – 338Combined sources6
Beta strandi343 – 345Combined sources3
Beta strandi356 – 361Combined sources6

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP44681.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini3 – 256OBG-type GAdd BLAST254

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

eggNOGiENOG4105C3G. Bacteria.
COG0012. LUCA.
KOiK06942.
OMAiCTIEPNI.
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. 1 hit.
InterProiIPR004396. ATPase_YchF/OLA1.
IPR012675. Beta-grasp_dom.
IPR013029. DUF933.
IPR031167. G_OBG.
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.
WP_005693776.1. 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.
WP_005693776.1. NC_000907.1.

3D structure databases

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

eggNOGiENOG4105C3G. Bacteria.
COG0012. LUCA.
KOiK06942.
OMAiCTIEPNI.
PhylomeDBiP44681.

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. 1 hit.
InterProiIPR004396. ATPase_YchF/OLA1.
IPR012675. Beta-grasp_dom.
IPR013029. DUF933.
IPR031167. G_OBG.
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...

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: November 2, 2016
This is version 126 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

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.