pbpC:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

pbpC

Gene Synonym(s)

ECK2515, b2519, JW2503, yfgN[1], yfgN

Product Desc.

putative peptidoglycan enzyme[2][3]

Penicillin-binding protein PBP1C murein transglycosylase[4]

Product Synonyms(s)

fused transglycosylase[1], transpeptidase[1], B2519[2][1], YfgN[2][1], PbpC[2][1], PBP1C[2][1] , ECK2515, JW2503, yfgN, b2519

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): pbpC[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]


PbpC has a penicillin-insensitive transglycosylase N-terminal domain. PbpC has a transpeptidase-like C-terminal domain that does not seem to be functional. PbpC is a membrane-bound periplasmic enzyme that has an uncleaved signal anchor[4]



Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


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

Standard name

pbpC

Mnemonic

Penicillin-binding protein

Synonyms

ECK2515, b2519, JW2503, yfgN[1], yfgN

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<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

56.97 minutes 

MG1655: 2645347..2643035
<gbrowseImage> name=NC_000913:2643035..2645347 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2568144..2565832
<gbrowseImage> name=NC_012967:2565832..2568144 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2528840..2531152
<gbrowseImage> name=NC_012759:2528840..2531152 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2645981..2643669
<gbrowseImage> name=NC_007779:2643669..2645981 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2737112..2734800
<gbrowseImage> name=NC_010473:2734800..2737112 source=DH10B preset=GeneLocation </gbrowseImage>

</protect>

Notes

Sequence Features

[back to top]


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

Feature Type Strain Genomic Location Evidence Reference Notes

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

ΔpbpC (Keio:JW2503)

deletion

deletion

PMID:16738554

Shigen


<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

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

</protect>

Notes

Genetic Resources

[back to top]


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

Resource Resource Type Source Notes/Reference

JW2503

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCCTCGCTTGTTAACCAAACG

Primer 2:CCTTGCATGACAAATTTCACTGT

2D5

Kohara Phage

Genobase

PMID:3038334

7F8

Kohara Phage

Genobase

PMID:3038334

purC80::Tn10

Linked marker

CAG18470 = CGSC7413[5]

est. P1 cotransduction: 10% [6]

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[5]

est. P1 cotransduction: 48% [6]
Synonyms:zff-208::Tn10

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:G7322

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14210

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003894

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947152

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3962

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008294

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name

PbpC

Synonyms

fused transglycosylase[1], transpeptidase[1], B2519[2][1], YfgN[2][1], PbpC[2][1], PBP1C[2][1] , ECK2515, JW2503, yfgN, b2519

Product description

putative peptidoglycan enzyme[2][3]

Penicillin-binding protein PBP1C murein transglycosylase[4]

EC number (for enzymes)

<protect></protect>

Notes

Function

[back to top]


<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:0030288

outer membrane-bounded periplasmic space

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0008360

regulation of cell shape

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0133

P

Seeded from EcoCyc (v14.0)

complete

GO:0008658

penicillin binding

PMID:1103132

IDA: Inferred from Direct Assay

F

Table 3 shows ampicillin inhibiting cell division when binding to PBP 3.

complete

GO:0009252

peptidoglycan biosynthetic process

PMID:7030331

IDA: Inferred from Direct Assay

P

Figure 2 shows formation of peptidoglycan when placed in a solution with penicillin binding protein 3.

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0573

P

Seeded from EcoCyc (v14.0)

complete

GO:0009274

peptidoglycan-based cell wall

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001264

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9906

C

Seeded from EcoCyc (v14.0)

complete

GO:0051781

positive regulation of cell division

PMID:1103132

IDA: Inferred from Direct Assay

P

Table 3 shows inhibition of cell division when penicillin binding protein 3 is competing with ampicillin.

complete

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

lon

PMID:16606699

Experiment(s):EBI-1143101

Protein

htpG

PMID:16606699

Experiment(s):EBI-1143101

Protein

rplB

PMID:16606699

Experiment(s):EBI-1143101

Protein

maeB

PMID:16606699

Experiment(s):EBI-1143101

Protein

groL

PMID:16606699

Experiment(s):EBI-1143101

Protein

rpsE

PMID:16606699

Experiment(s):EBI-1143101

Protein

clpB

PMID:16606699

Experiment(s):EBI-1143101

</protect>

Notes

Localization

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

Compartment Description Evidence Reference/Source Notes

Inner membrane

PMID:10542235

EchoLocation:pbpC

membrane


<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<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

MPRLLTKRGC WITLAAAPFL LFLAAWGADK LWPLPLHEVN PARVVVAQDG TPLWRFADAD
GIWRYPVTIE DVSPRYLEAL INYEDRWFWK HPGVNPFSVA RAAWQDLTSG RVISGGSTLT
MQVARLLDPH PKTFGGKIRQ LWRALQLEWH LSKREILTLY LNRAPFGGTL QGIGAASWAY
LGKSPANLSY SEAAMLAVLP QAPSRLRPDR WPERAEAARN KVLERMAVQG VWSREQVKES
REEPIWLAPR QMPQLAPLFS RMMLGKSKSD KITTTLDAGL QRRLEELAQN WKGRLPPRSS
LAMIVVDHTD MRVRGWVGSV DLNDDSRFGH VDMVNSIRSP GSVLKPFVYG LALDEGLIHP
ASLLQDVPRR TGDYRPGNFD SGFHGPISMS EALVRSLNLP AVQVLEAYGP KRFAAKLRNV
GLPLYLPNGA APNLSLILGG AGAKLEDMAA AYTAFARHGK AGKLRLQPDD PLLERPLMSS
GAAWIIRRIM ADEAQPLPDS ALPRVAPLAW KTGTSYGYRD AWAIGVNARY VIGIWTGRPD
GTPVVGQFGF ASAVPLLNQV NNILLSRSAN LPEDPRPNSV TRGVICWPGG QSLPEGDGNC
RRRLATWLLD GSQPPTLLLP EQEGINGIRF PIWLDENGKR VAADCPQARQ EMINVWPLPL
EPWLPASERR AVRLPPASTS CPPYGHDAQL PLQLTGVRDG AIIKRLPGAA EATLPLQSSG
GAGERWWFLN GEPLTERGRN VTLHLTDKGD YQLLVMDDVG QIATVKFVMQ
Length

770

Mol. Wt

85.068 kDa

pI

9.9 (calculated)

Extinction coefficient

172,340 - 172,965 (calc based on 16 Y, 27 W, and 5 C residues)


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

301..548

PF00905 Penicillin binding protein transpeptidase domain

PMID:19920124

Domain

49..227

PF00912 Transglycosylase

PMID:19920124

Domain

681..767

PF06832 Penicillin-Binding Protein C-terminus Family

PMID:19920124

<motif_map/>

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

Structures

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

Models

View models at:

</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


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

Resource type Source Notes/Reference

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16130444

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947152

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008294

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76577

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7322

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14210

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947152

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003894

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3962

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]


See Help:Cellular levels

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

Protein

E. coli K-12 MG1655

18

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

11

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

2a

molecules/cell/generation

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

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

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

Transcription unit(s)

pbpC

Figure courtesy of RegulonDB

</protect>

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

[back to top]


<protect><gbrowseImage> name=NC_000913:2645327..2645367 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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

[back to top]


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

Allele Name Mutation Phenotype Reference


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

Type Reference Notes

microarray

GEO Profiles:b2519 (EcoliWiki Page)

NCBI GEO profiles for pbpC

microarray

GenExpDB:b2519 (EcoliWiki Page)

Summary of data for pbpC from multiple microarray studies


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

Resource Name Resource Type Description Source Notes

<protect></protect>

Notes

Accessions Related to pbpC Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:G7322

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3962

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2519

EcoGene

EcoGene:EG14210

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003894

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008294

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


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

Organism Homologs (Statistics) Comments

Xenopus tropicalis

  • ENSXETP00000040947 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

E. coli O157

PBPC

From ECOO157CYC


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


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

Database Accession Notes

Pfam (EcoliWiki Page)

PF00905 Penicillin binding protein transpeptidase domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:56601

Pfam (EcoliWiki Page)

PF00912 Transglycosylase

Pfam (EcoliWiki Page)

PF06832 Penicillin-Binding Protein C-terminus Family

EcoCyc

EcoCyc:G7322

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14210

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003894

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3962

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008294

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


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

  1. 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 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

[back to top]