Reviewed, UniProtKB/Swiss-Prot P12735 (RL4_HALMA)

Names and origin

Protein names

Recommended name:
    50S ribosomal protein L4P
Alternative name(s):
    Hmal4
    Hl6

Gene names

Name:	rpl4p
Synonyms:	rpl4
Ordered Locus Names:	rrnAC1610

Organism

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

Taxonomic identifier

2238 [NCBI]

Taxonomic lineage

Archaea › Euryarchaeota › Halobacteria › Halobacteriales › Halobacteriaceae › Haloarcula

Protein attributes

Sequence length	246 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 By similarity. Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit. HAMAP MF_01328 Forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L22. Contacts the macrolide antibiotic spiramycin in the polypeptide exit tunnel. HAMAP MF_01328
Subunit structure	Part of the 50S ribosomal subunit. Interacts weakly with proteins L18e, L24 and L37e. Has been cross-linked to L18e. Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12
Sequence similarities	Belongs to the ribosomal protein L4P family.

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 – 246

246

50S ribosomal protein L4P HAMAP MF_01328

PRO_0000129329

Experimental info

Sequence conflict

154

1

V → K AA sequence Ref.3

Secondary structure

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246

Helix Strand Turn

Details...

Beta strand

2 – 6

5

Beta strand

12 – 17

6

Helix

20 – 23

4

Helix

28 – 40

13

Turn

50 – 54

5

Beta strand

63 – 66

4

Helix

104 – 117

14

Helix

121 – 126

6

Beta strand

137 – 140

4

Helix

142 – 146

5

Helix

150 – 159

10

Helix

163 – 169

7

Helix

178 – 182

5

Beta strand

193 – 199

7

Turn

202 – 206

5

Beta strand

211 – 214

4

Turn

215 – 217

3

Helix

220 – 223

4

Helix

225 – 227

3

Beta strand

233 – 236

4

Helix

237 – 243

7

Sequences

	Sequence		Length	Mass (Da)
	P12735-1 [UniParc]. Last modified January 4, 2005. Version 4. Checksum: 4BCA2FE20EE24EDF	FASTA	246	26,420
	10 20 30 40 50 60 MQATIYDLDG NTDGEVDLPD VFETPVRSDL IGKAVRAAQA NRKQDYGSDE YAGLRTPAES 70 80 90 100 110 120 FGSGRGQAHV PKQDGRARRV PQAVKGRSAH PPKTEKDRSL DLNDKERQLA VRSALAATAD 130 140 150 160 170 180 ADLVADRGHE FDRDEVPVVV SDDFEDLVKT QEVVSLLEAL DVHADIDRAD ETKIKAGQGS 190 200 210 220 230 240 ARGRKYRRPA SILFVTSDEP STAARNLAGA DVATASEVNT EDLAPGGAPG RLTVFTESAL AEVAER

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Organization and nucleotide sequence of a gene cluster coding for eight ribosomal proteins in the archaebacterium Halobacterium marismortui." Arndt E., Kroemer W., Hatakeyama T. J. Biol. Chem. 265:3034-3039(1990) [PubMed: 2406244] [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]	"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 1-28 AND 153-181.
[4]	"Localization of proteins HL29 and HL31 from Haloarcula marismortui within the 50 S ribosomal subunit by chemical crosslinking." Bergmann U., Wittmann-Liebold B. J. Mol. Biol. 232:693-700(1993) [PubMed: 8345527] [Abstract] Cited for: PROTEIN SEQUENCE OF 34-47; 86-117 AND 176-200, CROSS-LINKING TO L18E.
[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 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.

Cross-references

Sequence databases

EMBLGenBankDDBJ

J05222 Genomic DNA. Translation: AAA86860.1.
AY596297 Genomic DNA. Translation: AAV46527.1.

PIR

R5HS6H. D35063.

RefSeq

YP_136233.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FFK	X-ray	2.40	C	3-246	[»]
1JJ2	X-ray	2.40	C	1-246	[»]
1K73	X-ray	3.01	E	1-246	[»]
1K8A	X-ray	3.00	E	1-246	[»]
1K9M	X-ray	3.00	E	1-246	[»]
1KC8	X-ray	3.01	E	1-246	[»]
1KD1	X-ray	3.00	E	1-246	[»]
1KQS	X-ray	3.10	C	1-246	[»]
1M1K	X-ray	3.20	E	1-246	[»]
1M90	X-ray	2.80	E	1-246	[»]
1N8R	X-ray	3.00	E	1-246	[»]
1NJI	X-ray	3.00	E	1-246	[»]
1Q7Y	X-ray	3.20	E	1-246	[»]
1Q81	X-ray	2.95	E	1-246	[»]
1Q82	X-ray	2.98	E	1-246	[»]
1Q86	X-ray	3.00	E	1-246	[»]
1QVF	X-ray	3.10	C	1-246	[»]
1QVG	X-ray	2.90	C	1-246	[»]
1S72	X-ray	2.40	C	1-246	[»]
1VQ4	X-ray	2.70	C	1-246	[»]
1VQ5	X-ray	2.60	C	1-246	[»]
1VQ6	X-ray	2.70	C	1-246	[»]
1VQ7	X-ray	2.50	C	1-246	[»]
1VQ8	X-ray	2.20	C	1-246	[»]
1VQ9	X-ray	2.40	C	1-246	[»]
1VQK	X-ray	2.30	C	1-246	[»]
1VQL	X-ray	2.30	C	1-246	[»]
1VQM	X-ray	2.30	C	1-246	[»]
1VQN	X-ray	2.40	C	1-246	[»]
1VQO	X-ray	2.20	C	1-246	[»]
1VQP	X-ray	2.25	C	1-246	[»]
1W2B	X-ray	3.50	C	1-246	[»]
1YHQ	X-ray	2.40	C	1-246	[»]
1YI2	X-ray	2.65	C	1-246	[»]
1YIJ	X-ray	2.60	C	1-246	[»]
1YIT	X-ray	2.80	C	1-246	[»]
1YJ9	X-ray	2.90	C	1-246	[»]
1YJN	X-ray	3.00	C	1-246	[»]
1YJW	X-ray	2.90	C	1-246	[»]
2B66	X-ray	5.90	F	1-246	[»]
2B9N	X-ray	6.76	F	1-246	[»]
2B9P	X-ray	6.46	F	1-246	[»]
2OTJ	X-ray	2.90	C	1-246	[»]
2OTL	X-ray	2.70	C	1-246	[»]
2QA4	X-ray	3.00	C	1-246	[»]
2QEX	X-ray	2.90	C	1-246	[»]
3CC2	X-ray	2.40	C	1-246	[»]
3CC4	X-ray	2.70	C	1-246	[»]
3CC7	X-ray	2.70	C	1-246	[»]
3CCE	X-ray	2.75	C	1-246	[»]
3CCJ	X-ray	2.70	C	1-246	[»]
3CCL	X-ray	2.90	C	1-246	[»]
3CCM	X-ray	2.55	C	1-246	[»]
3CCQ	X-ray	2.90	C	1-246	[»]
3CCR	X-ray	3.00	C	1-246	[»]
3CCS	X-ray	2.95	C	1-246	[»]
3CCU	X-ray	2.80	C	1-246	[»]
3CCV	X-ray	2.90	C	1-246	[»]
3CD6	X-ray	2.75	C	1-246	[»]
3CMA	X-ray	2.80	C	1-246	[»]
3CME	X-ray	2.95	C	1-246	[»]
3CPW	X-ray	2.70	C	1-246	[»]
3CXC	X-ray	3.00	C	1-246	[»]
3G4S	X-ray	3.20	C	1-246	[»]
3G6E	X-ray	2.70	C	1-246	[»]
3G71	X-ray	2.85	C	1-246	[»]

ModBase

Search...

Genome annotation databases

GeneID

3128386.

GenomeReviews

Gene locus rrnAC1610 in contig AY596297_GR.

KEGG

hma:rrnAC1610.

NMPDR

fig|272569.1.peg.1501.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

P12735.

OMA

KGKMRGR.

Enzyme and pathway databases

BioCyc

HMAR272569:RRNAC1610-MON.

Family and domain databases

HAMAP

MF_01328.
[Tree]

InterPro

IPR002136. Ribosomal_L4/L1e.
IPR013000. Ribosomal_L4/L1e_euk/arc_CS.
IPR019970. Ribosomall_L4P.
[Graphical view]

Pfam

PF00573. Ribosomal_L4. 1 hit.
[Graphical view]

TIGRFAMs

TIGR03672. Rpl4p_arch. 1 hit.

PROSITE

PS00939. RIBOSOMAL_L1E. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RL4_HALMA

Accession

Primary (citable) accession number: P12735
Secondary accession number(s): Q5V1S5

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1989
Last sequence update:	January 4, 2005
Last modified:	November 3, 2009
This is version 81 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)