Page last updated: 2024-10-24
periplasmic space
Definition
Target type: cellularcomponent
The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria). [GOC:go_curators, GOC:md]
The periplasmic space is a compartment found in Gram-negative bacteria and some Gram-positive bacteria, located between the inner (cytoplasmic) membrane and the outer membrane. It is a gel-like matrix that contains a variety of proteins, enzymes, and other molecules. The periplasm plays a crucial role in many cellular processes, including:
- **Transport of molecules:** The periplasm serves as a pathway for the transport of nutrients, ions, and other molecules across the outer membrane. It contains transport proteins that facilitate the uptake of essential nutrients and the export of waste products.
- **Cell wall synthesis:** The periplasm is the site of synthesis of the peptidoglycan layer, a major component of the bacterial cell wall.
- **Signal transduction:** The periplasm can act as a site for the detection and transduction of environmental signals, such as changes in nutrient availability or the presence of toxins.
- **Degradation of macromolecules:** Some periplasmic enzymes are involved in the degradation of macromolecules, such as proteins and polysaccharides.
- **Defense against environmental stresses:** The periplasm can act as a buffer against environmental stresses, such as osmotic shock or changes in pH.
The periplasmic space is a highly dynamic compartment that is constantly changing in response to the needs of the cell. Its composition and function can vary depending on the bacterial species and its environment.
**Key components of the periplasmic space include:**
- **Peptidoglycan:** A rigid mesh-like structure that provides structural support for the cell.
- **Periplasmic proteins:** A diverse group of proteins involved in a wide range of cellular functions, including transport, enzymatic activity, and signal transduction.
- **Lipopolysaccharide (LPS):** A complex molecule found in the outer membrane of Gram-negative bacteria, which plays a role in cell wall integrity and interaction with the environment.
- **Periplasmic binding proteins:** Proteins that bind to specific molecules, such as nutrients or toxins, and facilitate their transport across the outer membrane.
- **Hydrolytic enzymes:** Enzymes involved in the degradation of macromolecules, such as proteins and polysaccharides.
The periplasm is a vital compartment for the survival and function of bacteria. It plays a key role in nutrient acquisition, cell wall biosynthesis, signal transduction, and defense against environmental stresses.'
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Proteins (3)
| Protein | Definition | Taxonomy |
|---|---|---|
| Thiamine-binding periplasmic protein | A thiamine-binding periplasmic protein that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P31550] | Escherichia coli K-12 |
| Histidine-binding periplasmic protein | A histidine-binding periplasmic protein that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0AEU0] | Escherichia coli K-12 |
| Beta-lactamase | A beta-lactamase that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P00811] | Escherichia coli K-12 |
Compounds (42)
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| thiamine | thiamine(1+) : A primary alcohol that is 1,3-thiazol-3-ium substituted by (4-amino-2-methylpyrimidin-5-yl)methyl, methyl and 2-hydroxyethyl groups at positions 3, 4 and 5, respectively. | primary alcohol; vitamin B1 | Escherichia coli metabolite; human metabolite; mouse metabolite; Saccharomyces cerevisiae metabolite |
| 1-anilino-8-naphthalenesulfonate | 1-anilino-8-naphthalenesulfonate: RN given refers to parent cpd 8-anilinonaphthalene-1-sulfonic acid : A naphthalenesulfonic acid that is naphthalene-1-sulfonic acid substituted by a phenylamino group at position 8. | aminonaphthalene; naphthalenesulfonic acid | fluorescent probe |
| 3-nitrobenzeneboronic acid | |||
| benzyl benzoate | benzyl benzoate : A benzoate ester obtained by the formal condensation of benzoic acid with benzyl alcohol. It has been isolated from the plant species of the genus Polyalthia. benzyl benzoate: structure; acarosan, a moist powder composed of wetted cellulose and benzyl benzoate, is used on carpets as an acaricide | benzoate ester; benzyl ester | acaricide; plant metabolite; scabicide |
| benzo(b)thiophene-2-boronic acid | benzo(b)thiophene-2-boronic acid: inhibits AmpC beta-lactamase; structure in first source | ||
| clotrimazole | conazole antifungal drug; imidazole antifungal drug; imidazoles; monochlorobenzenes | antiinfective agent; environmental contaminant; xenobiotic | |
| econazole | 1-{2-(4-chlorobenzyloxy)-2-(2,4-dichlorophenyl)ethyl}imidazole : A member of the class of imidazoles that is 1-(2,4-dichlorophenyl)-2-(imidazol-1-yl)ethanol in which the hydroxyl hydrogen is replaced by a 4-chlorobenzyl group. econazole : A racemate composed of equimolar amounts of (R)- and (S)-econazole. Used (as its nitrate salt) to treat skin infections such as athlete's foot, jock itch, ringworm and other fungal skin infections. Econazole: An imidazole derivative that is commonly used as a topical antifungal agent. | dichlorobenzene; ether; imidazoles; monochlorobenzenes | |
| fluconazole | fluconazole : A member of the class of triazoles that is propan-2-ol substituted at position 1 and 3 by 1H-1,2,4-triazol-1-yl groups and at position 2 by a 2,4-difluorophenyl group. It is an antifungal drug used for the treatment of mucosal candidiasis and for systemic infections including systemic candidiasis, coccidioidomycosis, and cryptococcosis. Fluconazole: Triazole antifungal agent that is used to treat oropharyngeal CANDIDIASIS and cryptococcal MENINGITIS in AIDS. | conazole antifungal drug; difluorobenzene; tertiary alcohol; triazole antifungal drug | environmental contaminant; P450 inhibitor; xenobiotic |
| glyburide | glyburide : An N-sulfonylurea that is acetohexamide in which the acetyl group is replaced by a 2-(5-chloro-2-methoxybenzamido)ethyl group. Glyburide: An antidiabetic sulfonylurea derivative with actions like those of chlorpropamide | monochlorobenzenes; N-sulfonylurea | anti-arrhythmia drug; EC 2.7.1.33 (pantothenate kinase) inhibitor; EC 3.6.3.49 (channel-conductance-controlling ATPase) inhibitor; hypoglycemic agent |
| gossypol | Gossypol: A dimeric sesquiterpene found in cottonseed (GOSSYPIUM). The (-) isomer is active as a male contraceptive (CONTRACEPTIVE AGENTS, MALE) whereas toxic symptoms are associated with the (+) isomer. | ||
| staurosporine aglycone | staurosporine aglycone: metabolite from culture broth of Nocardiopsis sp.; a neurotrophin antag; inhibits BDNF TrkB receptor | ||
| ketoconazole | 1-acetyl-4-(4-{[2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine : A dioxolane that is 1,3-dioxolane which is substituted at positions 2, 2, and 4 by imidazol-1-ylmethyl, 2,4-dichlorophenyl, and [para-(4-acetylpiperazin-1-yl)phenoxy]methyl groups, respectively. | dichlorobenzene; dioxolane; ether; imidazoles; N-acylpiperazine; N-arylpiperazine | |
| mefenamic acid | mefenamic acid : An aminobenzoic acid that is anthranilic acid in which one of the hydrogens attached to the nitrogen is replaced by a 2,3-dimethylphenyl group. Although classed as a non-steroidal anti-inflammatory drug, its anti-inflammatory properties are considered to be minor. It is used to relieve mild to moderate pain, including headaches, dental pain, osteoarthritis and rheumatoid arthritis. Mefenamic Acid: A non-steroidal anti-inflammatory agent with analgesic, anti-inflammatory, and antipyretic properties. It is an inhibitor of cyclooxygenase. | aminobenzoic acid; secondary amino compound | analgesic; antipyretic; antirheumatic drug; EC 1.14.99.1 (prostaglandin-endoperoxide synthase) inhibitor; environmental contaminant; non-steroidal anti-inflammatory drug; xenobiotic |
| miconazole | 1-[2-(2,4-dichlorobenzyloxy)-2-(2,4-dichlorophenyl)ethyl]imidazole : A member of the class of imidazoles that is 1-(2,4-dichlorophenyl)-2-(imidazol-1-yl)ethanol in which the hydroxyl hydrogen is replaced by a 2,4-dichlorobenzyl group. miconazole : A racemate composed of equimolar amounts of (R)- and (S)-miconazole. Used (as its nitrate salt) to treat skin infections such as athlete's foot, jock itch, ringworm and other fungal skin infections. It inhibits the synthesis of ergosterol, a critical component of fungal cell membranes. Miconazole: An imidazole antifungal agent that is used topically and by intravenous infusion. | dichlorobenzene; ether; imidazoles | |
| nicardipine | 2-[benzyl(methyl)amino]ethyl methyl 2,6-dimethyl-4-(3-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate : A dihydropyridine that is 1,4-dihydropyridine substituted by a methyl, {2-[benzyl(methyl)amino]ethoxy}carbonyl, 3-nitrophenyl, methoxycarbonyl and methyl groups at positions 2, 3, 4, 5 and 6, respectively. nicardipine : A racemate comprising equimolar amounts of (R)- and (S)-nicardipine. It is a calcium channel blocker which is used to treat hypertension. Nicardipine: A potent calcium channel blockader with marked vasodilator action. It has antihypertensive properties and is effective in the treatment of angina and coronary spasms without showing cardiodepressant effects. It has also been used in the treatment of asthma and enhances the action of specific antineoplastic agents. | benzenes; C-nitro compound; diester; dihydropyridine; methyl ester; tertiary amino compound | |
| oxaprozin | oxaprozin : A monocarboxylic acid that is a propionic acid derivative having a 4,5-diphenyl-1,3-oxazol-2-yl substituent at position 3. It is non-steroidal anti-inflammatory drug commonly used to relieve the pain and inflammatory responses associated with osteoarthritis and rheumatoid arthritis. Oxaprozin: An oxazole-propionic acid derivative, cyclooxygenase inhibitor, and non-steroidal anti-inflammatory drug that is used in the treatment of pain and inflammation associated with of OSTEOARTHRITIS; RHEUMATOID ARTHRITIS; and ARTHRITIS, JUVENILE. | 1,3-oxazoles; monocarboxylic acid | analgesic; non-steroidal anti-inflammatory drug |
| sulconazole | 1-{2-[(4-chlorobenzyl)sulfanyl]-2-(2,4-dichlorophenyl)ethyl}-1H-imidazole : A member of the class of imidazoles that is 1-ethyl-1H-imidazole in which one of the hydrogens of the methyl group is replaced by a (4-chlorobenzyl)sulfanediyl group while a second is replaced by a 2,4-dichlorophenyl group. sulconazole : A racemate comprising equimolar amounts of (R)- and (S)-sulconazole. An antifungal agent with activity against Candida species, it is used (generally as the nitrate salt) for the topical treatment of fungal skin infections. sulconazole: RN given refers to cpd with unspecified isomeric designation; structure given in first source | dichlorobenzene; imidazoles; monochlorobenzenes; organic sulfide | |
| delavirdine | delavirdine : The amide resulting from the formal condensation of 5-[(methylsulfonyl)amino]-1H-indole-2-carboxylic acid and 4-amino group of 1-[3-(isopropylamino)pyridin-2-yl]piperazine, delavirdine is a non-nucleoside reverse transcriptase inhibitor with activity specific for HIV-1. Viral resistance emerges rapidly when delavirdine is used alone, so it is therefore used (as the methanesulfonic acid salt) with other antiretrovirals for combination therapy of HIV infection. Delavirdine: A potent, non-nucleoside reverse transcriptase inhibitor with activity specific for HIV-1. | aminopyridine; indolecarboxamide; N-acylpiperazine; sulfonamide | antiviral drug; HIV-1 reverse transcriptase inhibitor |
| histidine | histidine : An alpha-amino acid that is propanoic acid bearing an amino substituent at position 2 and a 1H-imidazol-4-yl group at position 3. Histidine: An essential amino acid that is required for the production of HISTAMINE. L-histidine : The L-enantiomer of the amino acid histidine. | amino acid zwitterion; histidine; L-alpha-amino acid; polar amino acid zwitterion; proteinogenic amino acid | algal metabolite; Escherichia coli metabolite; human metabolite; micronutrient; mouse metabolite; nutraceutical; Saccharomyces cerevisiae metabolite |
| boric acid | boric acids | astringent | |
| thiophene-2-carboxylate | thiophene-2-carboxylic acid : A thiophenecarboxylic acid in which the carboxy group is located at position 2. | thiophenecarboxylic acid | |
| congo red | Congo Red : An indicator dye that is blue-violet at pH 3.0 and red at pH 5.0. Congo Red: An acid dye used in testing for hydrochloric acid in gastric contents. It is also used histologically to test for AMYLOIDOSIS. | bis(azo) compound | |
| diphenylborinic acid | diphenylborinic acid: structure given in first source | ||
| n-butylboronic acid | |||
| benzeneboronic acid | boronic acids | ||
| iodophthalein | |||
| 4-bromophenylboric acid | |||
| 3-aminobenzeneboronic acid | |||
| tazobactam | tazobactam : A member of the class of penicillanic acids that is sulbactam in which one of the exocyclic methyl hydrogens is replaced by a 1,2,3-triazol-1-yl group; used (in the form of its sodium salt) in combination with ceftolozane sulfate for treatment of complicated intra-abdominal infections and complicated urinary tract infections. Tazobactam: A penicillanic acid and sulfone derivative and potent BETA-LACTAMASE inhibitor that enhances the activity of other anti-bacterial agents against beta-lactamase producing bacteria. | penicillanic acids; triazoles | antiinfective agent; antimicrobial agent; EC 3.5.2.6 (beta-lactamase) inhibitor |
| sulbactam | penicillanic acids | ||
| 4-amino-3-hydroxybenzoic acid | |||
| methaneboronic acid | |||
| n-dansyl-3-aminobenzeneboronic acid | N-dansyl-3-aminobenzeneboronic acid: potent serine protease inhibitor; fluorescent boronic acid which reversibly binds to bacterial cell walls; structure given in first source | ||
| 4-methoxyphenylboronic acid | 4-methoxyphenylboronic acid: structure in first source | ||
| 1,4-phenylenebis(boronic acid) | 1,4-phenylenebis(boronic acid): structure in first source | ||
| 2-formylphenylboronic acid | 2-formylphenylboronic acid: structure in first source | ||
| thiophene-3-boronic acid | thiophene-3-boronic acid: structure in first source | ||
| quercetin | 7-hydroxyflavonol; pentahydroxyflavone | antibacterial agent; antineoplastic agent; antioxidant; Aurora kinase inhibitor; chelator; EC 1.10.99.2 [ribosyldihydronicotinamide dehydrogenase (quinone)] inhibitor; geroprotector; phytoestrogen; plant metabolite; protein kinase inhibitor; radical scavenger | |
| clavulanic acid | clavulanate : The conjugate base of clavulanic acid. clavulanic acid : Antibiotic isolated from Streptomyces clavuligerus. It acts as a suicide inhibitor of bacterial beta-lactamase enzymes. Clavulanic Acid: A beta-lactam antibiotic produced by the actinobacterium Streptomyces clavuligerus. It is a suicide inhibitor of bacterial beta-lactamase enzymes. Administered alone, it has only weak antibacterial activity against most organisms, but given in combination with other beta-lactam antibiotics it prevents antibiotic inactivation by microbial lactamase. | oxapenam | antibacterial drug; anxiolytic drug; bacterial metabolite; EC 3.5.2.6 (beta-lactamase) inhibitor |
| rottlerin | rottlerin : A chromenol that is 2,2-dimethyl-2H-chromene substituted by hydroxy groups at positions 5 and 7, a 3-acetyl-2,4,6-trihydroxy-5-methylbenzyl group at position 6 and a (1E)-3-oxo-1-phenylprop-1-en-3-yl group at position 8. A potassium channel opener, it is isolated from Mallotus philippensis. rottlerin: an angiogenesis inhibitor; an inhibitor of protein kinase Cdelta (PKCdelta) and calmodulin kinase III; RN refers to (E)-isomer; do not confuse this chalcone with an anthraquinone that is also called rottlerin (RN 481-72-1); | aromatic ketone; benzenetriol; chromenol; enone; methyl ketone | anti-allergic agent; antihypertensive agent; antineoplastic agent; apoptosis inducer; K-ATP channel agonist; metabolite |
| tazobactam sodium | tazobactam sodium : An organic sodium salt having tazobactam(1-) as the counterion; used in combination with ceftolozane sulfate for treatment of complicated intra-abdominal infections and complicated urinary tract infections. | organic sodium salt | antiinfective agent; antimicrobial agent; EC 3.5.2.6 (beta-lactamase) inhibitor |
| l 701324 | L 701324: a glycine/NMDA receptor antagonist | quinolines |