P56029 (RL1_HELPY) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
50S ribosomal protein L1

Gene names

Name:	rplA
Ordered Locus Names:	HP_1201

Organism

Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori) [Reference proteome] [HAMAP]

Taxonomic identifier

85962 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › delta/epsilon subdivisions › Epsilonproteobacteria › Campylobacterales › Helicobacteraceae › Helicobacter › Helicobacter pylori

Protein attributes

Sequence length	234 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Binds directly to 23S rRNA. The L1 stalk is quite mobile in the ribosome, and is involved in E site tRNA release By similarity. HAMAP-Rule MF_01318 Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA By similarity. HAMAP-Rule MF_01318 Peptides originating from the N-terminal end of L1 have antibacterial activity against bacteria such as E.coli and B.megaterium and modest antifungal activities. Has no effect on H.pylori itself. Peptides are not hemolytic against mammalian cells. These peptides may be released in the stomach during altruistic lysis to kill other fast growing bacteria. HAMAP-Rule MF_01318
Subunit structure	Part of the 50S ribosomal subunit.
Miscellaneous	The antimicrobial peptide HP (2-20) forms a short alpha-helix. Increasing the amphiphilicity of the helix increases its antimicrobial activities. HAMAP-Rule MF_01318
Sequence similarities	Belongs to the ribosomal protein L1P family.

Ontologies

Keywords
Biological process	Translation regulation
Ligand	RNA-binding rRNA-binding tRNA-binding
Molecular function	Antibiotic Antimicrobial Repressor Ribonucleoprotein Ribosomal protein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	defense response to bacterium Inferred from electronic annotation. Source: UniProtKB-KW regulation of translation Inferred from electronic annotation. Source: UniProtKB-KW translation Inferred from electronic annotation. Source: HAMAP
Cellular_component	large ribosomal subunit Inferred from electronic annotation. Source: InterPro
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...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 234

234

50S ribosomal protein L1 HAMAP-Rule MF_01318

PRO_0000125667

Natural variations

Natural variant

155

1

S → T in strain: Hp921023.

Experimental info

Mutagenesis

17 – 19

3

QND → WNW: Increases antibacterial and antifungal activities 2-4 fold without an increase in hemolytic activies. Ref.5

Secondary structure

1

.

.

.

234

Helix Strand Turn

Details...

Helix

6 – 18

13

Sequences

	Sequence		Length	Mass (Da)
	P56029 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: BC7CECDB6B0B0EA8	FASTA	234	25,266
	10 20 30 40 50 60 MAKKVFKRLE KLFSKIQNDK AYGVEQGVEV VKSLASAKFD ETVEVALRLG VDPRHADQMV 70 80 90 100 110 120 RGAVVLPHGT GKKVRVAVFA KDIKQDEAKN AGADVVGGDD LAEEIKNGRI DFDMVIATPD 130 140 150 160 170 180 MMAVVGKVGR ILGPKGLMPN PKTGTVTMDI AKAVSNAKSG QVNFRVDKKG NVHAPIGKAS 190 200 210 220 230 FPEEKIKENM LELVKTINRL KPSSAKGKYI RNAALSLTMS PSVSLDAQEL MDIK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The complete genome sequence of the gastric pathogen Helicobacter pylori." Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G., Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A., Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N., Loftus B.J., Richardson D.L., Dodson R.J. , Khalak H.G., Glodek A., McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E., Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D., Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S., Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C. Nature 388:539-547(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700392 / 26695.
[2]	"Isolation of recombinant protective Helicobacter pylori antigens." Hocking D., Webb E., Radcliff F., Rothel L., Taylor S., Pinczower G., Kapouleas C., Braley H., Lee A., Doidge C. Infect. Immun. 67:4713-4719(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 57-234. Strain: Hp921023.
[3]	"Antibacterial peptide from H. pylori." Putsep K., Branden C.I., Boman H.G., Normark S. Nature 398:671-672(1999) [PubMed] [Europe PMC] [Abstract] Cited for: SYNTHESIS, ANTIBACTERIAL ACTIVITY OF 2-20 AND 22-38.
[4]	"Structure of antimicrobial peptide, HP (2-20) and its analogues derived from Helicobacter pylori, as determined by 1H NMR spectroscopy." Lee K.H., Lee D.G., Park Y., Hahm K.-S., Kim Y. Submitted (SEP-2004) to the PDB data bank Cited for: STRUCTURE BY NMR OF 2-20.
[5]	"Interactions between the plasma membrane and the antimicrobial peptide HP (2-20) and its analogues derived from Helicobacter pylori." Lee K.H., Lee D.G., Park Y., Kang D.-I., Shin S.Y., Hahm K.-S., Kim Y. Biochem. J. 394:105-114(2006) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 2-20, ANTIFUNGAL ACTIVITY, LYSIS MECHANISM, MUTAGENESIS OF 17-GLN--ASP-19.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE000511 Genomic DNA. Translation: AAD08247.1.
U86609 Genomic DNA. Translation: AAB47277.1.

PIR

A64670.

RefSeq

NP_207992.1. NC_000915.1.
YP_006935121.1. NC_018939.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1OT0	NMR	-	A	2-18	[»]
1P0G	NMR	-	A	2-20	[»]
1P0J	NMR	-	A	2-20	[»]
1P0L	NMR	-	A	2-20	[»]
1P0O	NMR	-	A	2-20	[»]
1P5K	NMR	-	A	2-20	[»]
1P5L	NMR	-	A	2-20	[»]

ProteinModelPortal

P56029.

SMR

P56029. Positions 7-227.

ModBase

Search...

Protein-protein interaction databases

STRING

85962.HP1201.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAD08247; AAD08247; HP_1201.

GeneID

13870401.
899963.

KEGG

heo:C694_06215.
hpy:HP1201.

PATRIC

20593761. VBIHelPyl33062_1258.

Phylogenomic databases

eggNOG

COG0081.

KO

K02863.

OMA

AKGRYVK.

ProtClustDB

PRK05424.

Family and domain databases

Gene3D

3.30.190.20. 2 hits.
3.40.50.790. 1 hit.

HAMAP

MF_01318_B. Ribosomal_L1_B.

InterPro

IPR005878. Ribosom_L1_bac-type.
IPR002143. Ribosomal_L1.
IPR016094. Ribosomal_L1_2-a/b-sand.
IPR016095. Ribosomal_L1_3-a/b-sand.
IPR023673. Ribosomal_L1_CS.
IPR023674. Ribosomal_L1_SF.
[Graphical view]

Pfam

PF00687. Ribosomal_L1. 1 hit.
[Graphical view]

PIRSF

PIRSF002155. Ribosomal_L1. 1 hit.

SUPFAM

SSF56808. Ribosomal_L1. 1 hit.

TIGRFAMs

TIGR01169. rplA_bact. 1 hit.

PROSITE

PS01199. RIBOSOMAL_L1. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P56029.

Entry information

Entry name

RL1_HELPY

Accession

Primary (citable) accession number: P56029
Secondary accession number(s): P94849

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	May 1, 2013
This is version 89 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program