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Protein

Nodulation protein D 2

Gene

nodD2

Organism
Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein predictedi

Functioni

NodD regulates the expression of the nodABCFE genes which encode other nodulation proteins. NodD is also a negative regulator of its own expression. Binds flavonoids as inducers.

Miscellaneous

There are at least three nodD genes in R.meliloti. They differ in their specificity of interaction with different flavonoids and, consequently, contribute to the nodulation of various plant host species to different extents.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi23 – 42H-T-H motifPROSITE-ProRule annotationAdd BLAST20

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionActivator, DNA-binding, Repressor
Biological processNodulation, Transcription, Transcription regulation

Names & Taxonomyi

Protein namesi
Recommended name:
Nodulation protein D 2
Gene namesi
Name:nodD2
Ordered Locus Names:RA0404
ORF Names:SMa0757
Encoded oniPlasmid pSymA (megaplasmid 1)0 Publication
OrganismiRhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Taxonomic identifieri266834 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeSinorhizobium/Ensifer groupSinorhizobium
Proteomesi
  • UP000001976 Componenti: Plasmid pSymA

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001057191 – 310Nodulation protein D 2Add BLAST310

Structurei

3D structure databases

ProteinModelPortaliP08719.
SMRiP08719.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini6 – 63HTH lysR-typePROSITE-ProRule annotationAdd BLAST58

Phylogenomic databases

HOGENOMiHOG000103695.
KOiK14657.
OMAiCPTNKQL.

Family and domain databases

CDDicd08462. PBP2_NodD. 1 hit.
Gene3Di1.10.10.10. 1 hit.
InterProiView protein in InterPro
IPR005119. LysR_subst-bd.
IPR037416. NodD_PBP2.
IPR000847. Tscrpt_reg_HTH_LysR.
IPR036388. WH-like_DNA-bd_sf.
IPR036390. WH_DNA-bd_sf.
PfamiView protein in Pfam
PF00126. HTH_1. 1 hit.
PF03466. LysR_substrate. 1 hit.
PRINTSiPR00039. HTHLYSR.
SUPFAMiSSF46785. SSF46785. 1 hit.
PROSITEiView protein in PROSITE
PS50931. HTH_LYSR. 1 hit.

Sequencei

Sequence statusi: Complete.

P08719-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRFRGLDLNL LVALDALMTE RKLTAAARRV KLSQPAMSAA IARLRTYFGD
60 70 80 90 100
ELFSMQGREL IPTPRAEALA PAVRDALLHI QLSVIAWDPI NPAQSDRRFR
110 120 130 140 150
IILSDFMTLV FFERVVERLA REAPGVSFEL LPLDDDPYEL LRRGDVDFLV
160 170 180 190 200
LPDLFMSSAH PKAKLFAEAL VCVGCPTNEQ LLGELSFEKY MSMGHVAAQF
210 220 230 240 250
GRALKPSFEQ WLLLEHGFKR RVELVVPGFT LIPPLLPHTN RIAIIPLRLV
260 270 280 290 300
KYFEQTIPLR IVKHPLPPLW FTEAVQWPAL HNKDPGNIWM REILLQEASR
310
SEFQGETSLE
Length:310
Mass (Da):35,327
Last modified:October 24, 2001 - v2
Checksum:i10EF405717C0B4D5
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti88D → E in strain: 41. 1
Natural varianti256T → A in strain: 41. 1
Natural varianti268P → S in strain: 41. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04474 Genomic DNA. Translation: CAA28162.1.
M29367 Genomic DNA. Translation: AAA26336.1.
AE006469 Genomic DNA. Translation: AAK65062.1.
PIRiB25788.
D95312.
RefSeqiNP_435650.1. NC_003037.1.
WP_010967394.1. NC_003037.1.

Genome annotation databases

EnsemblBacteriaiAAK65062; AAK65062; SMa0757.
GeneIDi1235224.
KEGGisme:SMa0757.
PATRICifig|266834.11.peg.422.

Similar proteinsi

Entry informationi

Entry nameiNODD2_RHIME
AccessioniPrimary (citable) accession number: P08719
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: October 24, 2001
Last modified: January 31, 2018
This is version 114 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Plasmid, Reference proteome