glnD:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

glnD

Gene Synonym(s)

ECK0165, b0167, JW0162, glnD5[1]

Product Desc.

GLND[2][3]

Bifunctional uridylyltransferase/uridylyl-removing enzyme; (UTase/UR); controls uridylylation state and activity of PII(GlnB)[4]

Product Synonyms(s)

uridylyltransferase[1], B0167[2][1], GlnD[2][1] , ECK0165, JW0162, b0167

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): dapD[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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GlnD has both a uridylyltransferase and a uridylyl-removing activity. The only known substrates for GlnD are the two PII proteins GlnB and GlnK. In both cases GlnD covalently modifies residue Tyr51 in the T-loop of the substrate thereby controlling the ability of GlnB and GlnK to interact with their specific targets. The activity of GlnD is controlled by the intracellular glutamine availability. Glutamine inhibits the transferase action of GlnD and as a consequence GlnB and GlnK are deuridylylated in N-sufficient conditions. [Comment provided by EcoTeam member Mike Merrick, 11.16.06][4]



Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

glnD

Mnemonic

Glutamine

Synonyms

ECK0165, b0167, JW0162, glnD5[1]

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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

4.01 minutes 

MG1655: 188650..185978
<gbrowseImage> name=NC_000913:185978..188650 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 191492..188820
<gbrowseImage> name=NC_012967:188820..191492 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 185977..188649
<gbrowseImage> name=NC_012759:185977..188649 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 188650..185978
<gbrowseImage> name=NC_007779:185978..188650 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 162754..160082
<gbrowseImage> name=NC_010473:160082..162754 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

glnD(del) (Keio:JW0162)

deletion

deletion

PMID:16738554

Shigen

glnD::Tn5KAN-2 (FB20031)

Insertion at nt 2325 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20031

does not contain pKD46

GlnD G93

G93L or G93V

loss of UTase activity

PMID:20363937

GlnD G94

G94D

loss of UTase activity

PMID:20363937

GlnD D107

D107A or D107V or D107Y

loss of UTase activity

PMID:20363937


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0162

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAATACCCTTCCAGAACAGTA

Primer 2:CCCCCTTTATCGTTTGGATTGAG

21C8

Kohara Phage

Genobase

PMID:3038334

12D5

Kohara Phage

Genobase

PMID:3038334

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[5]

est. P1 cotransduction: 21% [6]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[5]

est. P1 cotransduction: 13% [6]
Synonyms:zae-502::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG11411

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11411

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944863

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001377

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1383

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000568

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

GlnD

Synonyms

uridylyltransferase[1], B0167[2][1], GlnD[2][1] , ECK0165, JW0162, b0167

Product description

GLND[2][3]

Bifunctional uridylyltransferase/uridylyl-removing enzyme; (UTase/UR); controls uridylylation state and activity of PII(GlnB)[4]

EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003607

F

Seeded from EcoCyc (v14.0)

complete

GO:0006807

nitrogen compound metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010043

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002912

P

Seeded from EcoCyc (v14.0)

complete

GO:0008773

(protein-PII) uridylyltransferase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00277

F

Seeded from EcoCyc (v14.0)

complete

GO:0008773

(protein-PII) uridylyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010043

F

Seeded from EcoCyc (v14.0)

complete

GO:0008773

(protein-PII) uridylyltransferase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.7.59

F

Seeded from EcoCyc (v14.0)

complete

GO:0016597

amino acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002912

F

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc (v14.0)

complete

GO:0016779

nucleotidyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002934

F

Seeded from EcoCyc (v14.0)

complete

GO:0016779

nucleotidyltransferase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013546

F

Seeded from EcoCyc (v14.0)

complete

GO:0016779

nucleotidyltransferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0548

F

Seeded from EcoCyc (v14.0)

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

glpD

PMID:16606699

Experiment(s):EBI-1135754

Protein

ytfM

PMID:16606699

Experiment(s):EBI-1135754

Protein

groL

PMID:16606699

Experiment(s):EBI-1135754

Protein

napC

PMID:16606699

Experiment(s):EBI-1135754

Protein

mukB

PMID:16606699

Experiment(s):EBI-1135754

Protein

alaS

PMID:16606699

Experiment(s):EBI-1135754

Protein

nadE

PMID:16606699

Experiment(s):EBI-1135754

Protein

lepA

PMID:16606699

Experiment(s):EBI-1135754

Protein

topA

PMID:16606699

Experiment(s):EBI-1135754

Protein

recF

PMID:16606699

Experiment(s):EBI-1135754

Protein

ulaD

PMID:16606699

Experiment(s):EBI-1135754
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MNTLPEQYAN TALPTLPGQP QNPCVWPRDE LTVGGIKAHI DTFQRWLGDA FDNGISAEQL
IEARTEFIDQ LLQRLWIEAG FSQIADLALV AVGGYGRGEL HPLSDVDLLI LSRKKLPDDQ
AQKVGELLTL LWDVKLEVGH SVRTLEECML EGLSDLTVAT NLIESRLLIG DVALFLELQK
HIFSEGFWPS DKFYAAKVEE QNQRHQRYHG TSYNLEPDIK SSPGGLRDIH TLQWVARRHF
GATSLDEMVG FGFLTSAERA ELNECLHILW RIRFALHLVV SRYDNRLLFD RQLSVAQRLN
YSGEGNEPVE RMMKDYFRVT RRVSELNQML LQLFDEAILA LPADEKPRPI DDEFQLRGTL
IDLRDETLFM RQPEAILRMF YTMVHNSAIT GIYSTTLRQL RHARRHLQQP LCNIPEARKL
FLSILRHPGA VRRGLLPMHR HSVLGAYMPQ WSHIVGQMQF DLFHAYTVDE HTIRVMLKLE
SFASEETRQR HPLCVDVWPR LPSTELIFIA ALFHDIAKGR GGDHSILGAQ DVVHFAELHG
LNSRETQLVA WLVRQHLLMS VTAQRRDIQD PEVIKQFAEE VQTENRLRYL VCLTVADICA
TNETLWNSWK QSLLRELYFA TEKQLRRGMQ NTPDMRERVR HHQLQALALL RMDNIDEEAL
HQIWSRCRAN YFVRHSPNQL AWHARHLLQH DLSKPLVLLS PQATRGGTEI FIWSPDRPYL
FAAVCAELDR RNLSVHDAQI FTTRDGMAMD TFIVLEPDGN PLSADRHEVI RFGLEQVLTQ
SSWQPPQPRR QPAKLRHFTV ETEVTFLPTH TDRKSFLELI ALDQPGLLAR VGKIFADLGI
SLHGARITTI GERVEDLFII ATADRRALNN ELQQEVHQRL TEALNPNDKG
Length

890

Mol. Wt

102.391 kDa

pI

6.7 (calculated)

Extinction coefficient

111,840 - 112,965 (calc based on 16 Y, 16 W, and 9 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

708..766

PF01842 ACT domain

PMID:19920124

Domain

815..877

PF01842 ACT domain

PMID:19920124

Domain

468..602

PF01966 HD domain

PMID:19920124

Domain

68..169

PF01909 Nucleotidyltransferase domain

PMID:19920124

Domain

192..331

PF08335 GlnD PII-uridylyltransferase

PMID:19920124

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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=glnD taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128160

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944863

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000568

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P27249

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11411

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11411

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944863

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001377

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1383

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

Ecoli K-12

7.718+/-0.202

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.028443114

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

188

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

167

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

100

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

dapD

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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:188630..188670 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b0167 (EcoliWiki Page)

NCBI GEO profiles for glnD

microarray

GenExpDB:b0167 (EcoliWiki Page)

Summary of data for glnD from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes
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Notes

Accessions Related to glnD Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG11411

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1383

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0167

EcoGene

EcoGene:EG11411

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001377

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000568

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Xenopus tropicalis

  • ENSXETP00000013506 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

GLND

From SHIGELLACYC

E. coli O157

GLND

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

Pfam (EcoliWiki Page)

PF01909 Nucleotidyltransferase domain

Pfam (EcoliWiki Page)

PF01966 HD domain

Pfam (EcoliWiki Page)

PF01842 ACT domain

Pfam (EcoliWiki Page)

PF01842 ACT domain

Panther (EcoliWiki Page)

PTHR13734:SF1

Superfamily (EcoliWiki Page)

SUPERFAMILY:55021

Superfamily (EcoliWiki Page)

SUPERFAMILY:55021

Superfamily (EcoliWiki Page)

SUPERFAMILY:81301

Superfamily (EcoliWiki Page)

SUPERFAMILY:81593

Superfamily (EcoliWiki Page)

SUPERFAMILY:81891

Pfam (EcoliWiki Page)

PF08335 GlnD PII-uridylyltransferase

EcoCyc

EcoCyc:EG11411

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11411

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001377

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1383

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000568

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

Categories

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