O25896 (NIKR_HELPY) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Putative nickel-responsive regulator

Gene names

Ordered Locus Names:

HP_1338

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	148 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Transcriptional regulator Potential. HAMAP-Rule MF_00476
Cofactor	Binds 1 nickel ion per subunit By similarity.
Subunit structure	Homotetramer By similarity.
Sequence similarities	Belongs to the transcriptional regulatory CopG/NikR family.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Ligand	DNA-binding Metal-binding Nickel
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	response to nickel cation Inferred from electronic annotation. Source: InterPro transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW nickel cation binding Inferred from electronic annotation. Source: HAMAP sequence-specific DNA binding transcription factor activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		1	EBI-528005,EBI-528005

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 148

148

Putative nickel-responsive regulator HAMAP-Rule MF_00476

PRO_0000139291

Sites

Metal binding

88

1

Nickel By similarity

Metal binding

99

1

Nickel By similarity

Metal binding

101

1

Nickel By similarity

Metal binding

107

1

Nickel By similarity

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

148

Helix Strand Turn

Details...

Beta strand

10 – 18

9

Helix

19 – 32

14

Helix

37 – 50

14

Beta strand

64 – 73

10

Beta strand

74 – 78

5

Helix

79 – 89

11

Beta strand

91 – 101

11

Beta strand

103 – 115

13

Helix

117 – 128

12

Beta strand

133 – 141

9

Helix

143 – 145

3

Sequences

	Sequence		Length	Mass (Da)
	O25896 [UniParc]. Last modified January 1, 1998. Version 1. Checksum: 9C8A2F803E7822B8	FASTA	148	17,147
	10 20 30 40 50 60 MDTPNKDDSI IRFSVSLQQN LLDELDNRII KNGYSSRSEL VRDMIREKLV EDNWAEDNPN 70 80 90 100 110 120 DESKIAVLVV IYDHHQRELN QRMIDIQHAS GTHVLCTTHI HMDEHNCLET IILQGNSFEI 130 140 QRLQLEIGGL RGVKFAKLTK ASSFEYNE

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.

+

Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AE000511 Genomic DNA. Translation: AAD08380.1.

PIR

B64687.

RefSeq

NP_208130.1. NC_000915.1.
YP_006935259.1. NC_018939.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2CA9	X-ray	2.05	A/B	1-148	[»]
2CAD	X-ray	2.30	A/B	1-148	[»]
2CAJ	X-ray	2.35	A/B	1-148	[»]
2WVB	X-ray	1.90	A/B	1-148	[»]
2WVC	X-ray	2.10	A/B	1-148	[»]
2WVD	X-ray	2.65	A/B/C/D	1-148	[»]
2WVE	X-ray	2.30	A/B	1-148	[»]
2WVF	X-ray	1.60	A/B	1-148	[»]
3LGH	X-ray	2.37	A/B/C/D	1-148	[»]
3PHT	X-ray	2.04	A/B	1-148	[»]
3QSI	X-ray	3.08	A/B/C/D/E/F/G/H/I/J	61-148	[»]

ProteinModelPortal

O25896.

SMR

O25896. Positions 9-147.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-3711N.

MINT

MINT-166516.

STRING

85962.HP1338.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAD08380; AAD08380; HP_1338.

GeneID

13870546.
900339.

KEGG

heo:C694_06905.
hpy:HP1338.

PATRIC

20594059. VBIHelPyl33062_1400.

Phylogenomic databases

eggNOG

COG0864.

KO

K07722.

OMA

DAHNCLE.

ProtClustDB

PRK00630.

Family and domain databases

Gene3D

1.10.1220.10. 1 hit.

HAMAP

MF_00476. NikR.

InterPro

IPR013321. Arc_rbn_hlx_hlx.
IPR002145. CopG.
IPR022988. Ni_resp_reg_NikR.
IPR010985. Ribbon_hlx_hlx.
IPR014864. TF_NikR_Ni-bd_C.
[Graphical view]

Pfam

PF08753. NikR_C. 1 hit.
PF01402. RHH_1. 1 hit.
[Graphical view]

SUPFAM

SSF47598. Met_repress_like. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

O25896.

Entry information

Entry name

NIKR_HELPY

Accession

Primary (citable) accession number: O25896

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 2, 2001
Last sequence update:	January 1, 1998
Last modified:	May 1, 2013
This is version 91 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program