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Protein

Ribosomal RNA small subunit methyltransferase Nep1

Gene

nep1

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Methyltransferase involved in ribosomal biogenesis. Specifically catalyzes the N1-methylation of pseudouridine at position 914 (Psi914) in 16S rRNA. Is not able to methylate uridine at this position.1 Publication

Catalytic activityi

S-adenosyl-L-methionine + pseudouridine(914) in 16S rRNA = S-adenosyl-L-homocysteine + N(1)-methylpseudouridine(914) in 16S rRNA.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei56 – 561Stabilizes Arg-54
Binding sitei162 – 1621S-adenosyl-L-methionine; via amide nitrogen
Binding sitei167 – 1671S-adenosyl-L-methionine; via carbonyl oxygen

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB
  • rRNA (pseudouridine) methyltransferase activity Source: UniProtKB
  • rRNA binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Ribosome biogenesis, rRNA processing

Keywords - Ligandi

RNA-binding, rRNA-binding, S-adenosyl-L-methionine

Enzyme and pathway databases

BRENDAi2.1.1.257. 3260.
2.1.1.260. 3260.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosomal RNA small subunit methyltransferase Nep1 (EC:2.1.1.-)
Alternative name(s):
16S rRNA (pseudouridine-N1-)-methyltransferase Nep1
16S rRNA Psi914 methyltransferase
Gene namesi
Name:nep1
Ordered Locus Names:MJ0557
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 205205Ribosomal RNA small subunit methyltransferase Nep1PRO_0000158616Add
BLAST

Interactioni

Subunit structurei

Homodimer.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei54 – 541Interaction with substrate rRNA
Sitei95 – 951Interaction with substrate rRNA
Sitei98 – 981Interaction with substrate rRNA
Sitei102 – 1021Interaction with substrate rRNA

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

STRINGi243232.MJ_0557.

Structurei

Secondary structure

1
205
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 119Combined sources
Helixi17 – 226Combined sources
Helixi36 – 394Combined sources
Turni40 – 456Combined sources
Helixi49 – 513Combined sources
Helixi55 – 6612Combined sources
Helixi69 – 724Combined sources
Beta strandi76 – 827Combined sources
Beta strandi85 – 906Combined sources
Helixi100 – 11112Combined sources
Beta strandi117 – 1237Combined sources
Helixi126 – 1327Combined sources
Beta strandi137 – 1415Combined sources
Beta strandi145 – 1473Combined sources
Helixi150 – 1556Combined sources
Beta strandi157 – 1626Combined sources
Beta strandi164 – 1674Combined sources
Helixi173 – 1753Combined sources
Beta strandi177 – 18812Combined sources
Helixi192 – 20413Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3BBDX-ray2.15A/B1-205[»]
3BBEX-ray2.20A/B1-205[»]
3BBHX-ray2.25A/B1-205[»]
ProteinModelPortaliQ57977.
SMRiQ57977. Positions 2-205.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ57977.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni141 – 1433S-adenosyl-L-methionine binding
Regioni185 – 1906S-adenosyl-L-methionine binding

Sequence similaritiesi

Belongs to the NEP1 family.Curated

Phylogenomic databases

eggNOGiarCOG04122. Archaea.
COG1756. LUCA.
InParanoidiQ57977.
KOiK14568.
OMAiLMAWTVC.
PhylomeDBiQ57977.

Family and domain databases

HAMAPiMF_00554. NEP1.
InterProiIPR029028. Alpha/beta_knot_MTases.
IPR005304. Rbsml_bgen_MeTrfase_EMG1/NEP1.
IPR023503. Ribosome_NEP1_arc.
[Graphical view]
PANTHERiPTHR12636. PTHR12636. 1 hit.
PfamiPF03587. EMG1. 1 hit.
[Graphical view]
SUPFAMiSSF75217. SSF75217. 1 hit.

Sequencei

Sequence statusi: Complete.

Q57977-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTYNIILAKS ALELIPEEIK NKIRKSRVYK YDILDSNYHY KAMEKLKDKE
60 70 80 90 100
MRGRPDIIHI SLLNILDSPI NHEKKLNIYI HTYDDKVLKI NPETRLPRNY
110 120 130 140 150
FRFLGVMEKV LKGERNHLIK MEEKTLEDLL NEINAKKIAI MTKTGKLTHP
160 170 180 190 200
KLLKEYDTFI IGGFPYGKLK INKEKVFGDI KEISIYNKGL MAWTVCGIIC

YSLSF
Length:205
Mass (Da):24,082
Last modified:November 1, 1996 - v1
Checksum:i8D3E8BFDCD502831
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98551.1.
PIRiE64369.

Genome annotation databases

EnsemblBacteriaiAAB98551; AAB98551; MJ_0557.
KEGGimja:MJ_0557.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98551.1.
PIRiE64369.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3BBDX-ray2.15A/B1-205[»]
3BBEX-ray2.20A/B1-205[»]
3BBHX-ray2.25A/B1-205[»]
ProteinModelPortaliQ57977.
SMRiQ57977. Positions 2-205.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ_0557.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB98551; AAB98551; MJ_0557.
KEGGimja:MJ_0557.

Phylogenomic databases

eggNOGiarCOG04122. Archaea.
COG1756. LUCA.
InParanoidiQ57977.
KOiK14568.
OMAiLMAWTVC.
PhylomeDBiQ57977.

Enzyme and pathway databases

BRENDAi2.1.1.257. 3260.
2.1.1.260. 3260.

Miscellaneous databases

EvolutionaryTraceiQ57977.

Family and domain databases

HAMAPiMF_00554. NEP1.
InterProiIPR029028. Alpha/beta_knot_MTases.
IPR005304. Rbsml_bgen_MeTrfase_EMG1/NEP1.
IPR023503. Ribosome_NEP1_arc.
[Graphical view]
PANTHERiPTHR12636. PTHR12636. 1 hit.
PfamiPF03587. EMG1. 1 hit.
[Graphical view]
SUPFAMiSSF75217. SSF75217. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
  2. "Backbone resonance assignments of the 48 kDa dimeric putative 18S rRNA-methyltransferase Nep1 from Methanocaldococcus jannaschii."
    Wurm J.P., Duchardt E., Meyer B., Leal B.Z., Kotter P., Entian K.D., Wohnert J.
    Biomol. NMR. Assign. 3:251-254(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NMR STUDIES.
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
  3. "The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase."
    Wurm J.P., Meyer B., Bahr U., Held M., Frolow O., Kotter P., Engels J.W., Heckel A., Karas M., Entian K.D., Wohnert J.
    Nucleic Acids Res. 38:2387-2398(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, RNA-BINDING, RNA-BINDING SITES.
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
  4. "The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site."
    Taylor A.B., Meyer B., Leal B.Z., Kotter P., Schirf V., Demeler B., Hart P.J., Entian K.D., Wohnert J.
    Nucleic Acids Res. 36:1542-1554(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF APOPROTEIN AND COMPLEXES WITH S-ADENOSYL-L-HOMOCYSTEINE AND SINEFUNGIN INHIBITOR, SUBUNIT, RNA-BINDING SITES.
    Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.

Entry informationi

Entry nameiNEP1_METJA
AccessioniPrimary (citable) accession number: Q57977
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 10, 2002
Last sequence update: November 1, 1996
Last modified: June 8, 2016
This is version 87 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, Reference proteome

Documents

  1. Methanococcus jannaschii
    Methanococcus jannaschii: 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.