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Protein

50S ribosomal protein L5

Gene

rpl5

Organism
Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809) (Halobacterium marismortui)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

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.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Keywords - Ligandi

RNA-binding, rRNA-binding, tRNA-binding

Enzyme and pathway databases

BioCyciHMAR272569:GJDH-1455-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
50S ribosomal protein L5
Alternative name(s):
Hl13
Hmal5
Gene namesi
Name:rpl5
Ordered Locus Names:rrnAC1598
OrganismiHaloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809) (Halobacterium marismortui)
Taxonomic identifieri272569 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaHalobacteriaHalobacterialesHalobacteriaceaeHaloarcula
ProteomesiUP000001169 Componenti: Chromosome I

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed2 Publications
Chaini2 – 17717650S ribosomal protein L5PRO_0000125051Add
BLAST

Interactioni

Subunit structurei

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).By similarity

Protein-protein interaction databases

STRINGi272569.rrnAC1598.

Structurei

Secondary structure

1
177
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni13 – 153Combined sources
Beta strandi18 – 2710Combined sources
Helixi39 – 457Combined sources
Beta strandi46 – 483Combined sources
Beta strandi51 – 544Combined sources
Turni60 – 623Combined sources
Beta strandi66 – 7611Combined sources
Helixi79 – 8810Combined sources
Helixi89 – 913Combined sources
Helixi96 – 983Combined sources
Beta strandi101 – 1033Combined sources
Beta strandi105 – 1073Combined sources
Beta strandi130 – 1367Combined sources
Helixi138 – 1436Combined sources
Beta strandi145 – 1484Combined sources
Helixi154 – 1563Combined sources
Helixi160 – 1689Combined sources
Turni169 – 1713Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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-ray3.50D2-177[»]
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[»]
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-ray3.00D2-177[»]
3G4SX-ray3.20D1-177[»]
3G6EX-ray2.70D1-177[»]
3G71X-ray2.85D1-177[»]
3I55X-ray3.11D1-177[»]
3I56X-ray2.90D1-177[»]
3OW2X-ray2.70D11-175[»]
4ADXelectron microscopy6.60D1-177[»]
4V4SX-ray6.76G2-177[»]
4V4TX-ray6.46G2-177[»]
4V9FX-ray2.40D1-177[»]
ProteinModelPortaliP14124.
SMRiP14124. Positions 11-175.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP14124.

Family & Domainsi

Sequence similaritiesi

Belongs to the ribosomal protein L5P family.Curated

Phylogenomic databases

eggNOGiCOG0094.
HOGENOMiHOG000231312.
KOiK02931.
OMAiKEESMEY.

Family and domain databases

Gene3Di3.30.1440.10. 1 hit.
HAMAPiMF_01333_A. Ribosomal_L5_A.
InterProiIPR002132. Ribosomal_L5.
IPR022804. Ribosomal_L5_arc.
IPR020929. Ribosomal_L5_CS.
IPR022803. Ribosomal_L5_domain.
[Graphical view]
PANTHERiPTHR11994. PTHR11994. 1 hit.
PfamiPF00281. Ribosomal_L5. 1 hit.
PF00673. Ribosomal_L5_C. 1 hit.
[Graphical view]
PIRSFiPIRSF002161. Ribosomal_L5. 1 hit.
SUPFAMiSSF55282. SSF55282. 1 hit.
PROSITEiPS00358. RIBOSOMAL_L5. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P14124-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSESESGGD FHEMREPRIE KVVVHMGIGH GGRDLANAED ILGEITGQMP
60 70 80 90 100
VRTKAKRTVG EFDIREGDPI GAKVTLRDEM AEEFLQTALP LAELATSQFD
110 120 130 140 150
DTGNFSFGVE EHTEFPSQEY DPSIGIYGLD VTVNLVRPGY RVAKRDKASR
160 170
SIPTKHRLNP ADAVAFIEST YDVEVSE
Length:177
Mass (Da):19,528
Last modified:January 23, 2007 - v4
Checksum:i565902FAA3D95FB6
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti134 – 1341N → R AA sequence (PubMed:2198942).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X58395 Genomic DNA. Translation: CAA41284.1.
AY596297 Genomic DNA. Translation: AAV46516.1.
PIRiS16535. R5HSL5.
RefSeqiWP_004957391.1. NC_006396.1.
YP_136222.1. NC_006396.1.

Genome annotation databases

EnsemblBacteriaiAAV46516; AAV46516; rrnAC1598.
GeneIDi3128287.
KEGGihma:rrnAC1598.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X58395 Genomic DNA. Translation: CAA41284.1.
AY596297 Genomic DNA. Translation: AAV46516.1.
PIRiS16535. R5HSL5.
RefSeqiWP_004957391.1. NC_006396.1.
YP_136222.1. NC_006396.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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-ray3.50D2-177[»]
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[»]
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-ray3.00D2-177[»]
3G4SX-ray3.20D1-177[»]
3G6EX-ray2.70D1-177[»]
3G71X-ray2.85D1-177[»]
3I55X-ray3.11D1-177[»]
3I56X-ray2.90D1-177[»]
3OW2X-ray2.70D11-175[»]
4ADXelectron microscopy6.60D1-177[»]
4V4SX-ray6.76G2-177[»]
4V4TX-ray6.46G2-177[»]
4V9FX-ray2.40D1-177[»]
ProteinModelPortaliP14124.
SMRiP14124. Positions 11-175.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi272569.rrnAC1598.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAV46516; AAV46516; rrnAC1598.
GeneIDi3128287.
KEGGihma:rrnAC1598.

Phylogenomic databases

eggNOGiCOG0094.
HOGENOMiHOG000231312.
KOiK02931.
OMAiKEESMEY.

Enzyme and pathway databases

BioCyciHMAR272569:GJDH-1455-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP14124.

Family and domain databases

Gene3Di3.30.1440.10. 1 hit.
HAMAPiMF_01333_A. Ribosomal_L5_A.
InterProiIPR002132. Ribosomal_L5.
IPR022804. Ribosomal_L5_arc.
IPR020929. Ribosomal_L5_CS.
IPR022803. Ribosomal_L5_domain.
[Graphical view]
PANTHERiPTHR11994. PTHR11994. 1 hit.
PfamiPF00281. Ribosomal_L5. 1 hit.
PF00673. Ribosomal_L5_C. 1 hit.
[Graphical view]
PIRSFiPIRSF002161. Ribosomal_L5. 1 hit.
SUPFAMiSSF55282. SSF55282. 1 hit.
PROSITEiPS00358. RIBOSOMAL_L5. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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. 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. 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.

Entry informationi

Entry nameiRL5_HALMA
AccessioniPrimary (citable) accession number: P14124
Secondary accession number(s): Q5V1T6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: January 23, 2007
Last modified: May 27, 2015
This is version 125 of the entry and version 4 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
  2. Ribosomal proteins
    Ribosomal proteins families and list of entries
  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.