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P14124

- RL5_HALMA

UniProt

P14124 - RL5_HALMA

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: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 120 (01 Oct 2014)
      Sequence version 4 (23 Jan 2007)
      Previous versions | rss
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    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

    1. rRNA binding Source: UniProtKB-HAMAP
    2. structural constituent of ribosome Source: InterPro
    3. tRNA binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. translation Source: UniProtKB-HAMAP

    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: Chromosome I

    Subcellular locationi

    GO - Cellular componenti

    1. ribosome Source: UniProtKB-KW

    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 – 153
    Beta strandi18 – 2710
    Beta strandi32 – 343
    Helixi39 – 457
    Beta strandi46 – 483
    Beta strandi51 – 544
    Turni60 – 623
    Beta strandi66 – 7611
    Helixi79 – 8810
    Helixi89 – 913
    Helixi96 – 983
    Beta strandi101 – 1033
    Beta strandi105 – 1073
    Helixi112 – 1143
    Beta strandi115 – 1184
    Beta strandi130 – 1367
    Helixi138 – 1436
    Beta strandi145 – 1484
    Helixi154 – 1563
    Helixi160 – 1689
    Turni169 – 1713

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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[»]
    2B9NX-ray6.76G2-177[»]
    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-ray3.00D2-177[»]
    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[»]
    4HUBX-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.
    OMAiPTRHKLT.

    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

    MSSESESGGD FHEMREPRIE KVVVHMGIGH GGRDLANAED ILGEITGQMP    50
    VRTKAKRTVG EFDIREGDPI GAKVTLRDEM AEEFLQTALP LAELATSQFD 100
    DTGNFSFGVE EHTEFPSQEY DPSIGIYGLD VTVNLVRPGY RVAKRDKASR 150
    SIPTKHRLNP ADAVAFIEST YDVEVSE 177
    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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X58395 Genomic DNA. Translation: CAA41284.1.
    AY596297 Genomic DNA. Translation: AAV46516.1.
    PIRiS16535. R5HSL5.
    RefSeqiYP_136222.1. NC_006396.1.

    Genome annotation databases

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

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X58395 Genomic DNA. Translation: CAA41284.1 .
    AY596297 Genomic DNA. Translation: AAV46516.1 .
    PIRi S16535. R5HSL5.
    RefSeqi YP_136222.1. NC_006396.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1FFK X-ray 2.40 D 2-177 [» ]
    1JJ2 X-ray 2.40 D 2-177 [» ]
    1K73 X-ray 3.01 F 2-177 [» ]
    1K8A X-ray 3.00 F 2-177 [» ]
    1K9M X-ray 3.00 F 2-177 [» ]
    1KC8 X-ray 3.01 F 2-177 [» ]
    1KD1 X-ray 3.00 F 2-177 [» ]
    1KQS X-ray 3.10 D 2-177 [» ]
    1M1K X-ray 3.20 F 2-177 [» ]
    1M90 X-ray 2.80 F 2-177 [» ]
    1N8R X-ray 3.00 F 2-177 [» ]
    1NJI X-ray 3.00 F 2-177 [» ]
    1Q7Y X-ray 3.20 F 2-177 [» ]
    1Q81 X-ray 2.95 F 2-177 [» ]
    1Q82 X-ray 2.98 F 2-177 [» ]
    1Q86 X-ray 3.00 F 2-177 [» ]
    1QVF X-ray 3.10 D 2-177 [» ]
    1QVG X-ray 2.90 D 2-177 [» ]
    1S72 X-ray 2.40 D 1-177 [» ]
    1VQ4 X-ray 2.70 D 1-177 [» ]
    1VQ5 X-ray 2.60 D 1-177 [» ]
    1VQ6 X-ray 2.70 D 1-177 [» ]
    1VQ7 X-ray 2.50 D 1-177 [» ]
    1VQ8 X-ray 2.20 D 1-177 [» ]
    1VQ9 X-ray 2.40 D 1-177 [» ]
    1VQK X-ray 2.30 D 1-177 [» ]
    1VQL X-ray 2.30 D 1-177 [» ]
    1VQM X-ray 2.30 D 1-177 [» ]
    1VQN X-ray 2.40 D 1-177 [» ]
    1VQO X-ray 2.20 D 1-177 [» ]
    1VQP X-ray 2.25 D 1-177 [» ]
    1W2B X-ray 3.50 D 2-177 [» ]
    1YHQ X-ray 2.40 D 1-177 [» ]
    1YI2 X-ray 2.65 D 1-177 [» ]
    1YIJ X-ray 2.60 D 1-177 [» ]
    1YIT X-ray 2.80 D 1-177 [» ]
    1YJ9 X-ray 2.90 D 1-177 [» ]
    1YJN X-ray 3.00 D 1-177 [» ]
    1YJW X-ray 2.90 D 1-177 [» ]
    2B9N X-ray 6.76 G 2-177 [» ]
    2B9P X-ray 6.46 G 2-177 [» ]
    2OTJ X-ray 2.90 D 1-177 [» ]
    2OTL X-ray 2.70 D 1-177 [» ]
    2QA4 X-ray 3.00 D 1-177 [» ]
    2QEX X-ray 2.90 D 1-177 [» ]
    3CC2 X-ray 2.40 D 1-177 [» ]
    3CC4 X-ray 2.70 D 1-177 [» ]
    3CC7 X-ray 2.70 D 1-177 [» ]
    3CCE X-ray 2.75 D 1-177 [» ]
    3CCJ X-ray 2.70 D 1-177 [» ]
    3CCL X-ray 2.90 D 1-177 [» ]
    3CCM X-ray 2.55 D 1-177 [» ]
    3CCQ X-ray 2.90 D 1-177 [» ]
    3CCR X-ray 3.00 D 1-177 [» ]
    3CCS X-ray 2.95 D 1-177 [» ]
    3CCU X-ray 2.80 D 1-177 [» ]
    3CCV X-ray 2.90 D 1-177 [» ]
    3CD6 X-ray 2.75 D 1-177 [» ]
    3CMA X-ray 2.80 D 1-177 [» ]
    3CME X-ray 2.95 D 1-177 [» ]
    3CPW X-ray 2.70 D 1-177 [» ]
    3CXC X-ray 3.00 D 2-177 [» ]
    3G4S X-ray 3.20 D 1-177 [» ]
    3G6E X-ray 2.70 D 1-177 [» ]
    3G71 X-ray 2.85 D 1-177 [» ]
    3I55 X-ray 3.11 D 1-177 [» ]
    3I56 X-ray 2.90 D 1-177 [» ]
    3OW2 X-ray 2.70 D 11-175 [» ]
    4ADX electron microscopy 6.60 D 1-177 [» ]
    4HUB X-ray 2.40 D 1-177 [» ]
    ProteinModelPortali P14124.
    SMRi P14124. Positions 11-175.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 272569.rrnAC1598.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAV46516 ; AAV46516 ; rrnAC1598 .
    GeneIDi 3128287.
    KEGGi hma:rrnAC1598.

    Phylogenomic databases

    eggNOGi COG0094.
    HOGENOMi HOG000231312.
    KOi K02931.
    OMAi PTRHKLT.

    Enzyme and pathway databases

    BioCyci HMAR272569:GJDH-1455-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P14124.

    Family and domain databases

    Gene3Di 3.30.1440.10. 1 hit.
    HAMAPi MF_01333_A. Ribosomal_L5_A.
    InterProi IPR002132. Ribosomal_L5.
    IPR022804. Ribosomal_L5_arc.
    IPR020929. Ribosomal_L5_CS.
    IPR022803. Ribosomal_L5_domain.
    [Graphical view ]
    PANTHERi PTHR11994. PTHR11994. 1 hit.
    Pfami PF00281. Ribosomal_L5. 1 hit.
    PF00673. Ribosomal_L5_C. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF002161. Ribosomal_L5. 1 hit.
    SUPFAMi SSF55282. SSF55282. 1 hit.
    PROSITEi PS00358. RIBOSOMAL_L5. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 120 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