Reviewed, UniProtKB/Swiss-Prot Q5SHN9 (RL4_THET8)

Names and origin

Protein names

Recommended name:
    50S ribosomal protein L4
Alternative name(s):
    L1e

Gene names

Name:	rplD
Ordered Locus Names:	TTHA1691

Organism

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) [Complete proteome] [HAMAP]

Taxonomic identifier

300852 [NCBI]

Taxonomic lineage

Bacteria › Deinococcus-Thermus › Deinococci › Thermales › Thermaceae › Thermus

Protein attributes

Sequence length	210 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome By similarity. Forms part of the polypeptide exit tunnel By similarity. This protein can be incorporated into E.coli ribosomes in vivo, which resulted in decreased peptidyltransferase (Ptase) activity of the hybrid ribosomes. The hybrid 50S subunits associate less well with 30S subunits to form the ribosome. HAMAP MF_01328
Subunit structure	Part of the 50S ribosomal subunit. HAMAP MF_01328
Post-translational modification	The N-terminus is blocked. HAMAP MF_01328
Sequence similarities	Belongs to the ribosomal protein L4P family.
Mass spectrometry	Molecular mass is 22724 Da from positions 1 - 210. Determined by MALDI. Ref.5

Ontologies

Keywords
Ligand	RNA-binding rRNA-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
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 210

210

50S ribosomal protein L4 HAMAP MF_01328

PRO_0000129300

Experimental info

Mutagenesis

55

1

G → A: Increases Ptase activity of hybrid ribosomes to a value greater than that of pure E.coli ribosomes. Increases binding of a tRNA analog to the P site. Ref.4

Mutagenesis

55

1

G → S: No effect on Ptase activity of hybrid ribosomes. No change in binding of a tRNA analog to the A or P site. Ref.4

Mutagenesis

56

1

E → A: Further decreases Ptase activity in E.coli hybrid ribosomes. Significantly decreases binding of a tRNA analog to the A or P site. Ref.4

Mutagenesis

56

1

E → Q: Restores Ptase activity of hybrid ribosomes to that of pure E.coli ribosomes. Significantly increases binding of a tRNA analog to the P site. Ref.4

Sequence conflict

19 – 20

2

EL → DV in AAA97862. Ref.1

Secondary structure

1

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210

Helix Strand Turn

Details...

Beta strand

7 – 11

5

Turn

12 – 14

3

Beta strand

15 – 19

5

Turn

26 – 28

3

Helix

31 – 44

14

Beta strand

68 – 71

4

Beta strand

77 – 79

3

Beta strand

81 – 85

5

Helix

103 – 121

19

Beta strand

122 – 124

3

Beta strand

131 – 134

4

Helix

136 – 145

10

Beta strand

154 – 159

6

Helix

161 – 166

6

Beta strand

170 – 176

7

Helix

183 – 188

6

Beta strand

189 – 195

7

Helix

197 – 209

13

Sequences

	Sequence		Length	Mass (Da)
	Q5SHN9-1 [UniParc]. Last modified December 21, 2004. Version 1. Checksum: BFB99AC179C110B4	FASTA	210	23,235
	10 20 30 40 50 60 MKEVAVYQIP VLSPSGRREL AADLPAEINP HLLWEVVRWQ LAKRRRGTAS TKTRGEVAYS 70 80 90 100 110 120 GRKIWPQKHT GRARHGDIGA PIFVGGGVVF GPKPRDYSYT LPKKVRKKGL AMAVADRARE 130 140 150 160 170 180 GKLLLVEAFA GVNGKTKEFL AWAKEAGLDG SESVLLVTGN ELVRRAARNL PWVVTLAPEG 190 200 210 LNVYDIVRTE RLVMDLDAWE VFQNRIGGEA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Direct linkage of str-, S10- and spc-related gene clusters in Thermus thermophilus HB8, and sequences of ribosomal proteins L4 and S10." Pfeiffer T., Jorcke D., Feltens R., Hartmann R.K. Gene 167:141-145(1995) [PubMed: 8566766] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Complete genome sequence of Thermus thermophilus HB8." Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S. Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"Identification of the 50S ribosomal proteins from the eubacterium Thermus thermophilus." Katsani K.R., Tsiboli P., Anagnostopoulos K., Urlaub H., Choli-Papadopoulou T. Biol. Chem. 381:1079-1087(2000) [PubMed: 11154066] [Abstract] Cited for: PROTEIN SEQUENCE OF 6-17, BLOCKAGE OF N-TERMINUS.
[4]	"On the structural and functional importance of the highly conserved Glu56 of Thermus thermophilus L4 ribosomal protein." Leontiadou F., Xaplanteri M.A., Papadopoulos G., Gerassimou C., Kalpaxis D.L., Choli-Papadopoulou T. J. Mol. Biol. 332:73-84(2003) [PubMed: 12946348] [Abstract] Cited for: MUTAGENESIS OF GLY-55 AND GLU-56.
[5]	"Extending ribosomal protein identifications to unsequenced bacterial strains using matrix-assisted laser desorption/ionization mass spectrometry." Suh M.-J., Hamburg D.M., Gregory S.T., Dahlberg A.E., Limbach P.A. Proteomics 5:4818-4831(2005) [PubMed: 16287167] [Abstract] Cited for: MASS SPECTROMETRY.
[6]	"The path of messenger RNA through the ribosome." Yusupova G.Z., Yusupov M.M., Cate J.H.D., Noller H.F. Cell 106:233-241(2001) [PubMed: 11511350] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (5.0 ANGSTROMS) OF THE RIBOSOME.
[7]	"Crystal structure of the ribosome at 5.5 A resolution." Yusupov M.M., Yusupova G.Z., Baucom A., Lieberman K., Earnest T.N., Cate J.H.D., Noller H.F. Science 292:883-896(2001) [PubMed: 11283358] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (5.5 ANGSTROMS) OF THE RIBOSOME.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

U36480 Genomic DNA. Translation: AAA97862.1.
AP008226 Genomic DNA. Translation: BAD71514.1.

RefSeq

YP_144957.2.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GIY	X-ray	5.50	F	1-210	[»]
1TWV	model	-	D	1-210	[»]
1YL3	X-ray	5.50	F	166-170	[»]
2HGJ	X-ray	5.00	F	1-210	[»]
2HGQ	X-ray	5.50	F	1-210	[»]
2HGU	X-ray	4.51	F	1-210	[»]
2J01	X-ray	2.80	F	1-210	[»]
2J03	X-ray	2.80	F	1-210	[»]
2V47	X-ray	3.80	F	1-210	[»]
2V49	X-ray	3.80	F	1-210	[»]
2WDI	X-ray	3.30	F	1-210	[»]
2WDJ	X-ray	3.30	F	1-210	[»]
2WDL	X-ray	3.50	F	1-210	[»]
2WDN	X-ray	3.50	F	1-210	[»]
2WH2	X-ray	3.45	F	1-210	[»]
2WH4	X-ray	3.45	F	1-210	[»]
3F1F	X-ray	3.00	F	1-210	[»]
3F1H	X-ray	3.00	F	1-210	[»]
3FIN	electron microscopy	6.40	F	1-208	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

Q5SHN9.

Genome annotation databases

GeneID

3167923.

GenomeReviews

Gene locus TTHA1691 in contig AP008226_GR.

KEGG

ttj:TTHA1691.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

Q5SHN9.

OMA

DIVRTER.

Enzyme and pathway databases

BioCyc

TTHE300852:TTHA1691-MON.

Family and domain databases

HAMAP

MF_01328.
[Tree]

InterPro

IPR015498. Ribosomal_L4.
IPR002136. Ribosomal_L4/L1e.
IPR013005. Ribosomal_L4/L1e_bac-type.
[Graphical view]

PANTHER

PTHR10746. Ribos_L4_L1E_bac. 1 hit.
PTHR10746:SF2. Ribosomal_L4. 1 hit.

Pfam

PF00573. Ribosomal_L4. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RL4_THET8

Accession

Primary (citable) accession number: Q5SHN9

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 29, 2005
Last sequence update:	December 21, 2004
Last modified:	November 3, 2009
This is version 46 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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