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P14124 (RL5_HALMA) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 116. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
50S ribosomal protein L5
Alternative name(s):
Hl13
Hmal5
Gene names
Name:rpl5
Ordered Locus Names:rrnAC1598
OrganismHaloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809) (Halobacterium marismortui) [Complete proteome] [HAMAP]
Taxonomic identifier272569 [NCBI]
Taxonomic lineageArchaeaEuryarchaeotaHalobacteriaHalobacterialesHalobacteriaceaeHaloarcula

Protein attributes

Sequence length177 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. HAMAP-Rule MF_01333_A

Subunit structure

Part of the 50S ribosomal subunit. Interacts with protein L18 and the 5S rRNA, and probably with tRNAs. Forms a bridge to the 30S subunit in the 70S ribosome By similarity. Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13

Sequence similarities

Belongs to the ribosomal protein L5P family.

Ontologies

Keywords
   LigandRNA-binding
rRNA-binding
tRNA-binding
   Molecular functionRibonucleoprotein
Ribosomal protein
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Gene Ontology (GO)
   Biological_processtranslation

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Cellular_componentribosome

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionrRNA binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

structural constituent of ribosome

Inferred from electronic annotation. Source: InterPro

tRNA binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.3 Ref.4
Chain2 – 17717650S ribosomal protein L5 HAMAP-Rule MF_01333_A
PRO_0000125051

Experimental info

Sequence conflict1341N → R AA sequence Ref.3

Secondary structure

....................................... 177
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P14124 [UniParc].

Last modified January 23, 2007. Version 4.
Checksum: 565902FAA3D95FB6

FASTA17719,528
        10         20         30         40         50         60 
MSSESESGGD FHEMREPRIE KVVVHMGIGH GGRDLANAED ILGEITGQMP VRTKAKRTVG 

        70         80         90        100        110        120 
EFDIREGDPI GAKVTLRDEM AEEFLQTALP LAELATSQFD DTGNFSFGVE EHTEFPSQEY 

       130        140        150        160        170 
DPSIGIYGLD VTVNLVRPGY RVAKRDKASR SIPTKHRLNP ADAVAFIEST YDVEVSE 

« Hide

References

« Hide 'large scale' references
[1]"Organization and nucleotide sequence of ten ribosomal protein genes from the region equivalent to the spectinomycin operon in the archaebacterium Halobacterium marismortui."
Scholzen T., Arndt E.
Mol. Gen. Genet. 228:70-80(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea."
Baliga N.S., Bonneau R., Facciotti M.T., Pan M., Glusman G., Deutsch E.W., Shannon P., Chiu Y., Weng R.S., Gan R.R., Hung P., Date S.V., Marcotte E., Hood L., Ng W.V.
Genome Res. 14:2221-2234(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
[3]"Amino acid sequences of the ribosomal proteins HL30 and HmaL5 from the archaebacterium Halobacterium marismortui."
Hatakeyama T., Hatakeyama T.
Biochim. Biophys. Acta 1039:343-347(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-177.
[4]"Extended N-terminal sequencing of proteins of archaebacterial ribosomes blotted from two-dimensional gels onto glass fiber and poly(vinylidene difluoride) membrane."
Walsh M.J., McDougall J., Wittmann-Liebold B.
Biochemistry 27:6867-6876(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 2-23.
[5]"The complete atomic structure of the large ribosomal subunit at 2.4 A resolution."
Ban N., Nissen P., Hansen J., Moore P.B., Steitz T.A.
Science 289:905-920(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 11-175 IN THE 50S SUBUNIT.
Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
[6]"The structural basis of ribosome activity in peptide bond synthesis."
Nissen P., Hansen J., Ban N., Moore P.B., Steitz T.A.
Science 289:920-930(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE 50S SUBUNIT.
Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
[7]"A pre-translocational intermediate in protein synthesis observed in crystals of enzymatically active 50S subunits."
Schmeing T.M., Seila A.C., Hansen J.L., Freeborn B., Soukup J.K., Scaringe S.A., Strobel S.A., Moore P.B., Steitz T.A.
Nat. Struct. Biol. 9:225-230(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT.
Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
[8]"The kink-turn: a new RNA secondary structure motif."
Klein D.J., Schmeing T.M., Moore P.B., Steitz T.A.
EMBO J. 20:4214-4221(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF THE 50S SUBUNIT.
Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
[9]"The structures of four macrolide antibiotics bound to the large ribosomal subunit."
Hansen J.L., Ippolito J.A., Ban N., Nissen P., Moore P.B., Steitz T.A.
Mol. Cell 10:117-128(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH FOUR MACROLIDE ANTIBIOTICS.
Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
[10]"Structural insights into peptide bond formation."
Hansen J.L., Schmeing T.M., Moore P.B., Steitz T.A.
Proc. Natl. Acad. Sci. U.S.A. 99:11670-11675(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE 50S SUBUNIT.
Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
[11]"Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit."
Hansen J.L., Moore P.B., Steitz T.A.
J. Mol. Biol. 330:1061-1075(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE 50S SUBUNIT IN COMPLEX WITH FIVE ANTIBIOTICS AT THE PEPTIDYL TRANSFERASE CENTER.
Strain: ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809.
[12]"Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit."
Schmeing T.M., Moore P.B., Steitz T.A.
RNA 9:1345-1352(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF THE 50S SUBUNIT WITH TWO DIFFERENT E SITE SUBSTRATES.
[13]"Revisiting the Haloarcula marismortui 50S ribosomal subunit model."
Gabdulkhakov A., Nikonov S., Garber M.
Acta Crystallogr. D 69:997-1004(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF THE 50S SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X58395 Genomic DNA. Translation: CAA41284.1.
AY596297 Genomic DNA. Translation: AAV46516.1.
PIRR5HSL5. S16535.
RefSeqYP_136222.1. NC_006396.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1FFKX-ray2.40D2-177[»]
1JJ2X-ray2.40D2-177[»]
1K73X-ray3.01F2-177[»]
1K8AX-ray3.00F2-177[»]
1K9MX-ray3.00F2-177[»]
1KC8X-ray3.01F2-177[»]
1KD1X-ray3.00F2-177[»]
1KQSX-ray3.10D2-177[»]
1M1KX-ray3.20F2-177[»]
1M90X-ray2.80F2-177[»]
1N8RX-ray3.00F2-177[»]
1NJIX-ray3.00F2-177[»]
1Q7YX-ray3.20F2-177[»]
1Q81X-ray2.95F2-177[»]
1Q82X-ray2.98F2-177[»]
1Q86X-ray3.00F2-177[»]
1QVFX-ray3.10D2-177[»]
1QVGX-ray2.90D2-177[»]
1S72X-ray2.40D1-177[»]
1VQ4X-ray2.70D1-177[»]
1VQ5X-ray2.60D1-177[»]
1VQ6X-ray2.70D1-177[»]
1VQ7X-ray2.50D1-177[»]
1VQ8X-ray2.20D1-177[»]
1VQ9X-ray2.40D1-177[»]
1VQKX-ray2.30D1-177[»]
1VQLX-ray2.30D1-177[»]
1VQMX-ray2.30D1-177[»]
1VQNX-ray2.40D1-177[»]
1VQOX-ray2.20D1-177[»]
1VQPX-ray2.25D1-177[»]
1W2BX-ray3.50D2-176[»]
1YHQX-ray2.40D1-177[»]
1YI2X-ray2.65D1-177[»]
1YIJX-ray2.60D1-177[»]
1YITX-ray2.80D1-177[»]
1YJ9X-ray2.90D1-177[»]
1YJNX-ray3.00D1-177[»]
1YJWX-ray2.90D1-177[»]
2B9PX-ray6.46G2-177[»]
2OTJX-ray2.90D1-177[»]
2OTLX-ray2.70D1-177[»]
2QA4X-ray3.00D1-177[»]
2QEXX-ray2.90D1-177[»]
3CC2X-ray2.40D1-177[»]
3CC4X-ray2.70D1-177[»]
3CC7X-ray2.70D1-177[»]
3CCEX-ray2.75D1-177[»]
3CCJX-ray2.70D1-177[»]
3CCLX-ray2.90D1-177[»]
3CCMX-ray2.55D1-177[»]
3CCQX-ray2.90D1-177[»]
3CCRX-ray3.00D1-177[»]
3CCSX-ray2.95D1-177[»]
3CCUX-ray2.80D1-177[»]
3CCVX-ray2.90D1-177[»]
3CD6X-ray2.75D1-177[»]
3CMAX-ray2.80D1-177[»]
3CMEX-ray2.95D1-177[»]
3CPWX-ray2.70D1-177[»]
3CXCX-ray3.00D2-176[»]
3G4SX-ray3.20D1-177[»]
3G6EX-ray2.70D1-177[»]
3G71X-ray2.85D1-177[»]
3I55X-ray3.11D1-177[»]
3I56X-ray2.90D1-177[»]
3OW2X-ray2.70D11-175[»]
4HUBX-ray2.40D1-177[»]
ProteinModelPortalP14124.
SMRP14124. Positions 11-175.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING272569.rrnAC1598.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAV46516; AAV46516; rrnAC1598.
GeneID3128287.
KEGGhma:rrnAC1598.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0094.
HOGENOMHOG000231312.
KOK02931.
OMAGNVCFGI.
ProtClustDBPRK04219.

Enzyme and pathway databases

BioCycHMAR272569:GJDH-1455-MONOMER.

Family and domain databases

Gene3D3.30.1440.10. 1 hit.
HAMAPMF_01333_A. Ribosomal_L5_A.
InterProIPR002132. Ribosomal_L5.
IPR022804. Ribosomal_L5_arc.
IPR020929. Ribosomal_L5_CS.
IPR022803. Ribosomal_L5_domain.
[Graphical view]
PANTHERPTHR11994. PTHR11994. 1 hit.
PfamPF00281. Ribosomal_L5. 1 hit.
PF00673. Ribosomal_L5_C. 1 hit.
[Graphical view]
PIRSFPIRSF002161. Ribosomal_L5. 1 hit.
SUPFAMSSF55282. SSF55282. 1 hit.
PROSITEPS00358. RIBOSOMAL_L5. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP14124.

Entry information

Entry nameRL5_HALMA
AccessionPrimary (citable) accession number: P14124
Secondary accession number(s): Q5V1T6
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 23, 2007
Last modified: March 19, 2014
This is version 116 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Ribosomal proteins

Ribosomal proteins families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references