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ecce/ periplasmic proteins/ enzymes
Oxidoreductases
-acting on hydrogen as donors
-acting on the CH-NH2 group of donors with oxygen as acceptor
-acting on NADH or NADPH with a nitrogenous group as acceptor
-acting on other nitrogenous compounds
-acting on various sulfoxide and N-oxide compounds
-acting on peroxide as acceptor
-acting on superoxide radicals as acceptor
-multicopper oxidases

Transferases
Aminoacyltransferase

Hydrolases
-acting on ester bonds:
---Phosphatases
---Sulfatases
-Glucosidases
-Aminohydrolases
-acting on peptide bonds
---Murein endopeptidases
---Metalloprotease
---Serine Proteases
-acting on other carbon-nitrogen bonds

Lyases
Carboxy Lyases

Isomerases
Proline Cis-Trans-Isomerases

Mutarotases

Disulfide Bond Formation



Oxidoreductases

Acting on hydrogen as donors

Hydrogenase-2 operon protein HybA (hybA )
functionperiplasmic electron-transferring activity of hydrogenase 2
interactionHybCO
cofactorsBinds 4 4Fe-4S clusters
regulation 
MW36003 Da; 328 aa


Hydrogenase-2 large chain (hybC )
functionNiFe hydrogenase, H2 + A = AH 2
interactionHybAO
cofactorsBinds 1 nickel ion per subunit
regulation 
MW62360 Da; 566 aa


Hydrogenase-2 small chain HybO (hybO )
functionNiFe hydrogenase Membrane-bound hydrogenase 2 small subunit
interactionHybAC
cofactorsBinds two 4Fe-4S clusters and one 3Fe-4S cluster
regulation 
MW39652 Da; 372 aa


Acting on the CH-NH2 Group of Donors With Oxygen as Acceptor

Copper amine oxidase precursor (maoA )
functioninitial steps of 2-phenylethylamine catabolism
Catalytic activity: 2-Phenylethylamine + H2O + O2 = Phenylacetaldehyde + NH3 + H2O2
interaction 
cofactorscopper and topaquinon
regulation 
structuredimer
PDB
MW84378 Da; 757 aa


Oxidoreductase Acting on NADH or NADPH with a Nitrogenous Group as Acceptor

Trimethylamine-N-oxide reductase precursor (torA )
functionreduces trimethylamine-n-oxide into trimethylamine, an anaerobic reaction coupled to energy yielding reaction
Catalytic activity: NADH + Trimethylamine-N-Oxide = NAD+ + Trimethylamine + H2O
interaction 
cofactorsmolybdopterin
regulation 
structure 
MW94456 Da; 848 aa


Oxidoreductase Acting on Other Nitrogenous Compounds

Nitrate reductase precursor (napA )
functiona role in anaerobic growth with limiting concentrations of nitrate, large subunit of the periplasmic nitrate reductase (NAP)
Catalytic activity: nitrite + acceptor = nitrate + reduced acceptor
interaction 
cofactorsmolybdopterin guanine dinucleotide (MGD)
regulationexpressed during anaerobic growth (via FNR), further induction by low concentrations of nitrate (via NarP)
MW93042 Da; 828 aa


Oxidoreductase Acting on acting on various sulfoxide and N-oxide compounds

Putative dimethyl sulfoxide reductase chain YnfE (ynfE )
functionDMSO reductase
interactionwith YfnF and YfnG
cofactorsMolybdenum (molybdopterin); may bind a 4Fe-4S cluster
regulation 
MW89780 Da; 808 aa


Putative dimethyl sulfoxide reductase chain YnfF (ynfF )
functionDMSO reductase
interactionwith YfnE and YfnG
cofactorsMolybdenum (molybdopterin); may bind a 4Fe-4S cluster
regulation 
MW89987 Da; 807 aa


Oxidoreductase Acting on a Peroxide as Acceptor

Thiol peroxidase precursor (tpx )
functionantioxidant, removing peroxides or H2O2
interaction 
cofactors 
regulation 
MW17704 Da; 167 aa


Oxidoreductase Acting on Superoxide Radicals as Acceptor

Superoxide dismutase precursor (sodC )
functiondestroys radicals
Catalytic activity: 2 Peroxide radical + 2 H+ = O2 + H2O2
interaction 
cofactors 
regulation 
structuremonomer
PDB
MW17681 Da; 173 aa


Multicopper Oxidase

Probable 53.4 kD blue copper oxidase precursor CueO (yacK )
functionMulticopper oxidase
interaction 
cofactors3 Cu
regulationvia CueR at elevated leveles of Cu
structuredimer
PDB
MW56556 Da; 516 aa


Transferases
 Aminoacyltransferase


Aminoacyltransferase precursor (ggt )
functionrole in glutathion degradation & synthesis,(g-Glutamyl cycle)
Catalytic activity: (5-L-glutamyl)-peptide + an amino acid = peptide + 5-L-glutamyl-amino acid
interaction 
cofactors 
regulation 
 consists of two polypeptide chains, which are synthesised from a single polypeptide
MW61768 Da, 580 aa


Hydrolases

 Acting on Ester Bonds:

Acyl-CoA thioesterase I precursor (tesA )
functionhydrolyzes only long chain (C12-C18) acyl thioesters
Catalytic activity: 2-lysophosphatidiylcholine + H2O = glycerophosphocholine + a fatty acid anion
interaction 
cofactors 
regulation 
  monomer
MW 23622 Da; 516 aa


2',3'-Cyclic-nucleotide 2'-phosphodiesterase precursor (cpdB )
functionbifunctional, catalyzes two consecutive reactions converting 2',3'-cyclic-nucleotide to 3'-nucleotide and then 3'-nucleotide to nucleic acid and phosphate
interaction 
cofactors 
regulation 
structuremonomer
PDB
MW70832 Da; 647 aa


Endonuclease I (endA )
functionEndonucleolytic cleavage to 5'-phosphodinucleotide and 5'-phosphooligonucleotides
interaction 
regulation 
 3d-structure
MW26709 Da; 2351 aa


Glycerophosphoryl diester posphodiesterase precursor (glpQ )
functionmultigene fam., hydrolyzes deacylated phospholiopids
Catalytic activity: a glycerophosphodiester + H2O = an alcohol + sn-glycerol 3-phosphate
interaction 
cofactors 
regulationGlpT, glycerol-3-phosphate inducible
MW40843 Da; 358 aa


Ribonuclease Iprecursor (rna )
functionCleaves the phosphodiester bond between any two nucleotides. Preference for cytidylic or guanylic acid.
interactiontwo isoforms encoded by same gene
cofactors 
regulation 
  four disulfide bonds
MW29617 Da; 268 aa


UDP-sugar hydrolase precursor (ushA )
functionmultifunctional: hydrolase, 5'-Nucleotidase
Catalytic activity 1: UDP-sugar + H(2)O = UMP + sugar 1-phosphate. Catalytic activity 2: A 5'-ribonucleotide + H(2)O = A ribonucleoside + orthophosphate
interaction 
cofactorsBinds two Zn2+; Co2+ for Nucleotidase
regulationinhibition by an intracellular protein inhibitor
structuremonomer
PDB
MW60824 Da; 550 aa


Phosphatases

pH 2.5 acid phosphatase precursor (appA )
functionCatalytic activity: an orthophosphoric monoester + H2O = an alcohol + orthophosphate
interaction 
cofactors 
regulationcAMP regulated, induced when reaching stationary phase, synthesis triggered by phosphate starvation or shift from aerobic to anaerobic condit.
 monomer
PDB
MW47056 Da; 432 aa


Glucose-1-phosphatase precursor (agp )
functionrequired for growth in high phosphate with G-1-P as sole carbon source
Catalytic activity: D-glucose 1-phosphate + H2O = D-GLUCOSE + orthophosphate
interaction 
cofactors 
regulationindependent from inorganic phosphate availability, catabolite repression, positively by cAMP/CRP,
 dimer
PDB
MW45683 Da; 413 aa


Class B acid phosphatase precursor (aphA )
functionBroad spectrum dephosphorylating enzyme
interaction 
cofactors 
regulationActivated by Mg2+ and ethanol; inhibited by EDTA, nucleosides, inorganic phosphate and Ca2+
 homotetramer
MW26103 Da; 237 aa


Alkaline phosphatase precursor (phoA )
functionBroad spectrum dephosphorylating enzyme

Extensively used as a reporter enzyme and in gene fusion experiments

interaction 
cofactorsmetalloenzyme containing two zinc atoms and a magnesium ion
regulationinduced by low phosphate
structurethree isoforms
dimer
PDB
MW49438 Da; 471 aa


Sulfatases

Putative sulfatase YdeN (ydeN )
functionbelongs to the sulfatase family
interaction 
cofactors 
regulation 
MW62802 Da; 560 aa


Glucosidases

Alpha-amylase precursor (malS )
functionAlpha-amylase; degradation of maltooligosaccharides with a preference for chain length longer than 6 glucose units
interaction 
cofactors 
regulation MalT (maltose regulon)
 monomer
2 disulfide bonds
MW75712 Da; 676 aa


Beta-glucosidase precursor (bglX )
functionhydrolysis of terminal non-reducing beta-D glucose residues
interaction 
cofactors 
regulation 
MW83460 Da; 765 aa


Probable bifunctional chitinase/lysozyme precursor (chiA )
functionhydrolysis of [[beta]]-1,4 glucosidic linkages between N-acetylmuramic acid and N-acetylglucosamine and/or chitin degradation
interaction 
cofactors 
regulation 
MW97057 Da; 897 aa


Lytic murein transglycosylase precursor (slt )
functionMurein-degrading, may play role in recaycling muropeptides during cell elongation and/or cell division
interactionenergy conserving reaction
cofactors 
regulation 
  PDB
MW73369 Da; 645 aa


Trehalase precursor (treA )
functionalpha- 1,1 glycosidic bond, to use trehalose as osmoprotectant
interaction 
cofactors 
regulationslightly induced by high osmolarity and stationary phase
MW63636 Da; 565 aa


Hydrolases Aminohydrolases

Putative L-asparaginase AsgX (ybiK )
functionL-asparagine + H 2O = L-aspartate + NH 3
interaction 
regulation 
structure PDB
MW33394 Da; 321 aa


Hydrolases Acting on Peptide Bonds

Murein Endopeptidases (Cell Wall Synthesis):

Penicillin-Binding Protein 4 precursor (dacB )
functionfinal stages in peptidoglycan synthesis
interactionpenicillin sensitive
cofactors 
regulation 
MW51798 Da; 477 aa


Penicillin-binding protein 5 precursor (dacA )
functionD-alanine carboxypeptidase
Removes C-terminal d-ala residues from sugar-peptide cell wall precursors
Belongs to Ser protease family S11
interaction 
cofactors 
regulation 
MW44444 Da; 403 aa


Penicillin-binding protein 6 precursor (dacC )
functionD-alanine carboxypeptidase
Removes C-terminal d-ala residues from sugar-peptide cell wall precursors
Belongs to Ser protease family S11
interaction 
cofactors 
regulation 
MW43609 Da; 400 aa


Penicillin-binding protein 7 precursor (pbpG )
functioncell wall formation
interactionpenicillin sensitieve
cofactors 
regulation 
MW34245 Da; 313 aa


Penicillin-insensitive murein endopeptidase precursor (mepA )
functionmurein removal from the sacculus, may faciliate integration of nascent murein strands into sacculus
interactionpenicillin insensitive
cofactors 
regulation 
MW30136 Da; 274 aa


Proteases

Metalloproteases

Alkaline phosphatase isozyme conversion protein IAP (iap or b2753 )
Peptidase familyM28C
Function 
Structure 
MW37920 Da
345 aa (1-24 signal pept.)


ProteaseIII precursor (ptr )
functionMay prefer small substrates
interaction 
cofactorsrequires divalent cations, binds Zn2+
regulation 
 monomer
MW107708 Da; 962 aa


Hypothetical protein YebA (yebA )
Peptidase familyM37 InterPro
Function 
Structure 
MW49057 Da
440 aa (1-34 signal pept.)


55.5 kD protein in kdgK-dctA intergenic region precursor (yhjJ )
functionmetalloprotease
interaction 
cofactorsbinds zinc?
regulation 
 has lost the active site residues
MW55527 Da; 498 aa


Serine Proteases

Protease DegP (Do) precursor (htrA )
functionrequired at high temp., degradation of damaged prot., chaperone activity at low temperature, shared specificity with DegQ
interaction 
cofactors 
regulationinduction by heat shock
structurehexamer
PDB
MW49439 Da; 474 aa


Protease DegQ precursor
(hhoA )
functionshared specificity with HtrA/DegP
interaction 
cofactors 
regulation 
MW47205 Da; 455 aa


Tail specific protease precursor (prc )
functionselectively degrades proteins with nonpolar C- terminus (that arises for example from the action of 10sRNA), PBP3 maturation
interaction 
cofactors 
regulation 
MW76663 Da; 682 aa


UmuD (umuD )
Peptidase familyS24 InterPro
Function 
Structure 
MW15063 Da
139 aa (1-24 signal pept.)


Hydrolase Acting on Carbon-Nitrogen Bonds, Others Than Above

Penicillin acylase precursor (ampC )
functionpenicillin resistance
Catalytic activity:
beta-lactam + H2O = a substituted beta-amino acid
the N4-C7 bond of the lactam ring is cleaved
interaction 
cofactors 
regulation 
structuremonomer
PDB
MW41555 Da; 377 aa


Penicillin-binding protein AmpH (ampH )
functionBinds penicillin & belongs to the beta-lactamase family
interaction 
cofactors 
regulation 
MW41849 Da; 385 aa


L-asparaginase II precursor (ansB )
functionaspartate synthesis
Catalytic activity: L-asparagine + H2O = L-aspartate + NH3
interaction 
cofactors 
regulationinduction by cAMP and anaerobiosis
structuretetramer
PDB
MW36850 Da, 348 aa


Penicillin acylase precursor (pac )
functionpenicillin resistance
Catalytic activity: penicillin + H2O = a fatty acid anion + 6-aminopenicillanate
interaction 
cofactors 
regulation 
 dimer
PDB
MW94642 Da; 846 aa


Probable N-acetylmuramoyl-L-alanine amidase YbjR (ybjR )
functionHydrolyzes the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides
interaction 
regulation 
MW31072 Da; 276 aa


Carboxy Lyase

Biosynthetic arginine decarboxylase precursor (ADC) (speA )
functionbiosynthetic and biodegradative form, first step in the spermidine synthesis from arginine, the biodegradive form may ply a role in regulating pH by consuming proteins
interaction 
cofactors pyridoxal phosphate and Mg2+
regulationinduction: growth in acidic enriched medium containing arginine (biodegr.), growth in MMA at neitral pH (biosynth.), repression of speA and feedback inhibition of ADC by putrescine and spermidine,
 homotetramer
MW73983 Da; 658 aa


Isomerases

Proline Cis-Trans-Isomerases (Folding Catalysts)

Peptidyl-prolyl cis-trans isomerase A precursor (ppiA )
functionaccelerate the folding of proteins
interaction 
cofactors 
regulationinhibition by cyclosporin A
structuremonomer
PDB
MW20431 Da; 190 aa


FkbP-type peptidyl-prolyl cis-trans isomerase FkpA precursor (fkpA )
functionfolding of extracytoplasmic proteins
interaction 
cofactors 
regulation 
MW28882 Da; 270 aa


Survival protein SurA precursor (surA )
functionfolding of extracytoplasmic proteins, essential in stationary phase
interaction 
cofactors 
regulation 
structurePDB
MW47283 Da; 428 aa


Mutarotases

Mutarotase (galM )
functionAldose 1-epimerase, converts alpha-aldose to the beta-anomer. Acts on D-glucose, L-arabinose, D-xylose, D-galactose, maltose and lactose.
interaction 
regulation 
MW38190 Da; 346 aa


Disulfide Bond Formation(Folding Catalysts)

Thiol:disulfide interchange protein DsbA precursor (dsbA )
functiondisulfide bond formation in e.g. PhoA, OmpA, pilus biogenesis
interactionreoxidised by DsbB
cofactors 
regulation 
structure PDB
MW23104 Da; 208 aa


Thiol:disulfide interchange Protein DsbC precursor (dsbC )
functiondisulfide bond formation, also acts as disulfide isomerase
interactionreoxidised by DsbD
cofactors 
regulation 
structuredimer
PDB
MW25622 Da; 236 aa


Thiol:disulfide interchange protein DsbE precursor (ccmG )
functiondisulfide bond formation, also acts as disulfide oxidoreductase in cytochrome c biogenensis
interaction 
cofactors 
regulation 
MW20809 Da; 185 aa


Thiol:disulfide interchange protein DsbG precursor (dsbG )
functioninvolved in disulfide bond formation
interaction 
cofactors 
regulation 
MW27495 Da; 248 aa