50S ribosomal protein L5P - Haloarcula marismortui

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Reviewed, UniProtKB/Swiss-Prot P14124 (RL5_HALMA)

Last modified November 3, 2009. Version 86. History...

Clusters with 100%, 90%, 50% identity |

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    50S ribosomal protein L5P
Alternative name(s):
    Hmal5
    Hl13

Gene names

Name:	rpl5p
Ordered Locus Names:	rrnAC1598

Organism

Haloarcula marismortui (Halobacterium marismortui) [Complete proteome] [HAMAP]

Taxonomic identifier

2238 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Halobacteria › Halobacteriales › Halobacteriaceae › Haloarcula

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Protein attributes

Sequence length	177 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

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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 MF_01333
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.
Sequence similarities	Belongs to the ribosomal protein L5P family.

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Ontologies

Keywords
Ligand	RNA-binding rRNA-binding tRNA-binding
Molecular function	Ribonucleoprotein Ribosomal protein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	translation Inferred from electronic annotation. Source: HAMAP
Cellular component	ribosome Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	rRNA binding Inferred from electronic annotation. Source: HAMAP structural constituent of ribosome Inferred from electronic annotation. Source: InterPro tRNA binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.3 Ref.4

Chain

2 – 177

176

50S ribosomal protein L5P HAMAP MF_01333

PRO_0000125051

Experimental info

Sequence conflict

134

N → R AA sequence Ref.3

Secondary structure

177

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P14124-1 [UniParc].

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

177

19,528

        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

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References

	« Hide 'large scale' referencesShow '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: 1832208] [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: 15520287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 43049 / DSM 3752 / JCM 8966.
[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: 2198942] [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: 3196689] [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: 10937989] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 11-175 IN THE 50S SUBUNIT. Strain: ATCC 43049 / DSM 3752 / JCM 8966.
[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: 10937990] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF THE 50S SUBUNIT. Strain: ATCC 43049 / DSM 3752 / JCM 8966.
[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: 11828326] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF THE 50S SUBUNIT. Strain: ATCC 43049 / DSM 3752 / JCM 8966.
[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: 11483524] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF THE 50S SUBUNIT. Strain: ATCC 43049 / DSM 3752 / JCM 8966.
[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: 12150912] [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.
[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: 12185246] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE 50S SUBUNIT. Strain: ATCC 43049 / DSM 3752 / JCM 8966.
[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: 12860128] [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.
[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: 14561884] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF THE 50S SUBUNIT WITH TWO DIFFERENT E SITE SUBSTRATES.
+	Additional computationally mapped references.

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Cross-references

Sequence databases

X58395 Genomic DNA. Translation: CAA41284.1.
AY596297 Genomic DNA. Translation: AAV46516.1.

PIR

R5HSL5. S16535.

RefSeq

YP_136222.1.

3D structure databases

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	2-176	[»]
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	[»]
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	2-176	[»]
3G4S	X-ray	3.20	D	1-177	[»]
3G6E	X-ray	2.70	D	1-177	[»]
3G71	X-ray	2.85	D	1-177	[»]

ModBase

Search...

Genome annotation databases

GeneID

3128287.

GenomeReviews

Gene locus rrnAC1598 in contig AY596297_GR.

KEGG

hma:rrnAC1598.

NMPDR

fig|272569.1.peg.1489.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

P14124.

OMA

KLVLNIC.

Enzyme and pathway databases

BioCyc

HMAR272569:RRNAC1598-MON.

Family and domain databases

HAMAP

MF_01333.
[Tree]

InterPro

IPR002132. Ribosomal_L5.
[Graphical view]

Gene3D

G3DSA:3.30.1440.10. Ribosomal_L5. 1 hit.

PANTHER

PTHR11994. Ribosomal_L5. 1 hit.

Pfam

PF00281. Ribosomal_L5. 1 hit.
PF00673. Ribosomal_L5_C. 1 hit.
[Graphical view]

PIRSF

PIRSF002161. Ribosomal_L5. 1 hit.

ProDom

PD013434. Ribosomal_L5_mit. 1 hit.
[Graphical view] [Entries sharing at least one domain]

PROSITE

PS00358. RIBOSOMAL_L5. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

RL5_HALMA

Accession

Primary (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:	November 3, 2009
This is version 86 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Ribosomal proteins

Ribosomal proteins families and list of entries

SIMILARITY comments

Index of protein domains and families