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Escherichia coli K-12 substr. MG1655 Polypeptide: glucan biosynthesis protein D

Gene: opgD Accession Numbers: EG12859 (EcoCyc), b1424, ECK1418

Synonyms: yzzZ, ydcG, mdoD

Regulation Summary Diagram: ?

Regulation summary diagram for opgD

The opgD gene was identified in silico as a paralog of opgG [Lequette04]. The protein was thought to be secreted to the periplasmic space via the twin-arginine translocation (Tat) pathway, but a tatC mutation does not affect its localization to the periplasmic space. OpgD thus can be exported by both the Tat and Sec pathways [TullmanErcek07].

A mutation in opgD does not cause gross changes in the synthesis or function of osmoregulated periplasmic glucans (OPGs), but alters the size of the glucose backbone of OPG molecules [Lequette04].

opgD: osmoregulated periplasmic glucan [Lequette04]
mdoD: membrane derived oligosaccharide

Locations: periplasmic space

Map Position: [1,494,880 -> 1,496,535] (32.22 centisomes, 116°)
Length: 1656 bp / 551 aa

Molecular Weight of Polypeptide: 62.758 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004754 , EchoBASE:EB2701 , EcoGene:EG12859 , EcoliWiki:b1424 , OU-Microarray:b1424 , PortEco:mdoD , PR:PRO_000023179 , Pride:P40120 , Protein Model Portal:P40120 , RefSeq:NP_415941 , RegulonDB:EG12859 , SMR:P40120 , String:511145.b1424 , UniProt:P40120

Relationship Links: InterPro:IN-FAMILY:IPR006311 , InterPro:IN-FAMILY:IPR007444 , InterPro:IN-FAMILY:IPR011013 , InterPro:IN-FAMILY:IPR013783 , InterPro:IN-FAMILY:IPR014438 , InterPro:IN-FAMILY:IPR014718 , InterPro:IN-FAMILY:IPR014756 , InterPro:IN-FAMILY:IPR019546 , InterPro:IN-FAMILY:IPR023724 , Pfam:IN-FAMILY:PF04349 , Prosite:IN-FAMILY:PS51318

In Paralogous Gene Group: 291 (2 members)

GO Terms:

Biological Process: GO:0032951 - regulation of beta-glucan biosynthetic process Inferred from experiment [Lequette04]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA01a]
GO:0009250 - glucan biosynthetic process Inferred by computational analysis [GOA06]
GO:0016051 - carbohydrate biosynthetic process Inferred by computational analysis [GOA01a]
GO:0051274 - beta-glucan biosynthetic process Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0030246 - carbohydrate binding Inferred by computational analysis [GOA01a]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space Inferred from experiment Inferred by computational analysis [DiazMejia09, Han14, LopezCampistrou05, Lequette04, TullmanErcek07]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a]


Essentiality data for opgD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Last-Curated ? 14-May-2007 by Keseler I , SRI International

Sequence Features

Protein sequence of glucan biosynthesis protein D with features indicated

Feature Class Location Common Name Citations Comment
Signal-Sequence 1 -> 32 signal sequence
Chain 33 -> 551  
UniProt: Glucans biosynthesis protein D;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Amanda Mackie on Thu Dec 19, 2013:
Membrane derived oligosaccharides (MDOs) are now called osmoregulated periplasmic glucans (OPGs) and gene names have been changed accordingly 20.12.2013
Ingrid Keseler on Fri Jun 8, 2007:
Gene start position corrected based on [Lequette04 ].
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
1/26/1998 (pkarp) Merged genes G6739/b1424 and EG12859/ydcG


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Han14: Han MJ, Kim JY, Kim JA (2014). "Comparison of the large-scale periplasmic proteomes of the Escherichia coli K-12 and B strains." J Biosci Bioeng 117(4);437-42. PMID: 24140104

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lequette04: Lequette Y, Odberg-Ferragut C, Bohin JP, Lacroix JM (2004). "Identification of mdoD, an mdoG paralog which encodes a twin-arginine-dependent periplasmic protein that controls osmoregulated periplasmic glucan backbone structures." J Bacteriol 186(12);3695-702. PMID: 15175282

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

TullmanErcek07: Tullman-Ercek D, DeLisa MP, Kawarasaki Y, Iranpour P, Ribnicky B, Palmer T, Georgiou G (2007). "Export pathway selectivity of Escherichia coli twin arginine translocation signal peptides." J Biol Chem 282(11);8309-16. PMID: 17218314

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Thu Sep 3, 2015, BIOCYC14A.