Reviewed, UniProtKB/Swiss-Prot Q5SHQ3 (RL6_THET8)

Names and origin

Protein names

Recommended name:
    50S ribosomal protein L6

Gene names

Name:	rplF
Ordered Locus Names:	TTHA1677

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

General annotation (Comments)

Function	This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center. HAMAP MF_01365
Subunit structure	Part of the 50S ribosomal subunit. HAMAP MF_01365
Sequence similarities	Belongs to the ribosomal protein L6P family.
Mass spectrometry	Molecular mass is 19401 Da from positions 2 - 180. Determined by MALDI. Ref.4

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

Initiator methionine

1

1

Removed Ref.3

Chain

2 – 180

179

50S ribosomal protein L6 HAMAP MF_01365

PRO_0000131072

Experimental info

Sequence conflict

16

1

S → Q Ref.2

Sequence conflict

18

1

E → Q Ref.2

Sequence conflict

19 – 20

2

VA → AV AA sequence Ref.3

Sequence conflict

20

1

A → S Ref.2

Sequence conflict

23

1

R → L Ref.2

Sequence conflict

25

1

K → L AA sequence Ref.3

Sequence conflict

27

1

K → Y AA sequence Ref.3

Sequence conflict

34

1

E → S in CAA39899. Ref.2

Sequence conflict

41 – 42

2

MR → LK in CAA39899. Ref.2

Sequence conflict

48

1

G → N in CAA39899. Ref.2

Sequence conflict

62

1

K → R in CAA39899. Ref.2

Sequence conflict

84

1

S → V in CAA39899. Ref.2

Sequence conflict

102 – 103

2

AL → SI in CAA39899. Ref.2

Sequence conflict

131

1

V → I in CAA39899. Ref.2

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

180

Helix Strand Turn

Details...

Beta strand

16 – 19

4

Beta strand

24 – 27

4

Beta strand

39 – 41

3

Helix

59 – 64

6

Helix

68 – 76

9

Beta strand

103 – 106

4

Beta strand

113 – 115

3

Beta strand

122 – 124

3

Beta strand

126 – 129

4

Beta strand

131 – 134

4

Helix

146 – 149

4

Beta strand

156 – 158

3

Sequences

	Sequence		Length	Mass (Da)
	Q5SHQ3-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 1913833C0C30E95D	FASTA	180	19,532
	10 20 30 40 50 60 MSRIGRLPIP VPKGVSVEVA PGRVKVKGPK GELEVPVSPE MRVVVEEGVV RVERPSDERR 70 80 90 100 110 120 HKSLHGLTRT LIANAVKGVS EGYSKELLIK GIGYRARLVG RALELTVGFS HPVVVEPPEG 130 140 150 160 170 180 ITFEVPEPTR VRVSGIDKQK VGQVAANIRA IRKPSAYHEK GIYYAGEPVR LKPGKAGAKK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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].
[2]	"Analysis of the spc ribosomal protein operon of Thermus aquaticus." Jahn O., Hartmann R.K., Erdmann V.A. Eur. J. Biochem. 197:733-740(1991) [PubMed: 2029902] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-131.
[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 2-29.
[4]	"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.
[5]	"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.
[6]	"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

AP008226 Genomic DNA. Translation: BAD71500.1.
X56552 Genomic DNA. Translation: CAA39899.1.

PIR

S15442.

RefSeq

YP_144943.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1GIY	X-ray	5.50	H	-	[»]
1YL3	X-ray	5.50	H	54-175	[»]
2HGJ	X-ray	5.00	H	-	[»]
2HGQ	X-ray	5.50	H	1-180	[»]
2HGU	X-ray	4.51	H	-	[»]
2J01	X-ray	2.80	H	2-179	[»]
2J03	X-ray	2.80	H	2-179	[»]
2V47	X-ray	3.80	H	2-179	[»]
2V49	X-ray	3.80	H	2-179	[»]
2WDI	X-ray	3.30	H	1-180	[»]
2WDJ	X-ray	3.30	H	1-180	[»]
2WDL	X-ray	3.50	H	1-180	[»]
2WDN	X-ray	3.50	H	1-180	[»]
2WH2	X-ray	3.45	H	1-180	[»]
2WH4	X-ray	3.45	H	1-180	[»]
3FIN	electron microscopy	6.40	H	12-171	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

Q5SHQ3.

Genome annotation databases

GeneID

3169807.

GenomeReviews

Gene locus TTHA1677 in contig AP008226_GR.

KEGG

ttj:TTHA1677.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

Q5SHQ3.

OMA

RTLVANM.

Enzyme and pathway databases

BioCyc

TTHE300852:TTHA1677-MON.

Family and domain databases

HAMAP

MF_01365.
[Tree]

InterPro

IPR000702. Ribosomal_L6.
IPR020040. Ribosomal_L6_a/b-dom.
IPR002358. Ribosomal_L6_CS.
IPR019906. Ribosomal_L6_sg.
[Graphical view]

Gene3D

G3DSA:3.90.930.12. Ribosomal_L6. 2 hits.

PANTHER

PTHR11655. Ribosomal_L6. 1 hit.

Pfam

PF00347. Ribosomal_L6. 2 hits.
[Graphical view]

PIRSF

PIRSF002162. Ribosomal_L6. 1 hit.

PRINTS

PR00059. RIBOSOMALL6.

ProDom

PD002236. Ribosomal_L6. 1 hit.
[Graphical view] [Entries sharing at least one domain]

TIGRFAMs

TIGR03654. L6_bact. 1 hit.

PROSITE

PS00525. RIBOSOMAL_L6_1. False negative.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RL6_THET8

Accession

Primary (citable) accession number: Q5SHQ3

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 29, 2005
Last sequence update:	January 23, 2007
Last modified:	November 3, 2009
This is version 44 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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