coenzyme PQQ biosynthesis enzyme PqqE; This model describes coenzyme PQQ biosynthesis protein ...
9-367
0e+00
coenzyme PQQ biosynthesis enzyme PqqE; This model describes coenzyme PQQ biosynthesis protein E, a prototypical peptide-cyclizing radical SAM enzyme. It links a Tyr to a Glu as the first step in the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ) from the precursor peptide PqqA. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
The actual alignment was detected with superfamily member TIGR02109:
Pssm-ID: 162708 [Multi-domain] Cd Length: 358 Bit Score: 550.10 E-value: 0e+00
coenzyme PQQ biosynthesis enzyme PqqE; This model describes coenzyme PQQ biosynthesis protein ...
9-367
0e+00
coenzyme PQQ biosynthesis enzyme PqqE; This model describes coenzyme PQQ biosynthesis protein E, a prototypical peptide-cyclizing radical SAM enzyme. It links a Tyr to a Glu as the first step in the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ) from the precursor peptide PqqA. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
Pssm-ID: 162708 [Multi-domain] Cd Length: 358 Bit Score: 550.10 E-value: 0e+00
Iron-sulfur cluster-binding SPASM domain of coenzyme PQQ synthesis protein E; Coenzyme PQQ ...
240-349
1.16e-74
Iron-sulfur cluster-binding SPASM domain of coenzyme PQQ synthesis protein E; Coenzyme PQQ synthesis protein E (PqqE), also called pyrroloquinoline quinone (PQQ) biosynthesis protein E or PqqA peptide cyclase (EC 1.21.98.4), is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the formation of a C-C bond between C-4 of glutamate and C-3 of tyrosine residues of the PqqA protein, which is the first enzymatic step in the biosynthesis of the bacterial enzyme cofactor PQQ. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM (RS) enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. PqqE contains two auxiliary Fe-S clusters in its SPASM domain: one nearest the RS site (AuxI) is in the form of a 2Fe-2S cluster ligated by four cysteines; and a more remote cluster (AuxII) in the form of a 4Fe-4S center that is ligated by three cysteine residues and one aspartate residue.
Pssm-ID: 410610 [Multi-domain] Cd Length: 114 Bit Score: 226.80 E-value: 1.16e-74
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
15-160
1.94e-43
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, chromosome partitioning, Coenzyme transport and metabolism];
Pssm-ID: 440301 [Multi-domain] Cd Length: 159 Bit Score: 148.13 E-value: 1.94e-43
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
20-162
3.45e-18
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.
Pssm-ID: 427681 [Multi-domain] Cd Length: 159 Bit Score: 80.65 E-value: 3.45e-18
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
19-183
4.20e-06
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.
Pssm-ID: 214792 [Multi-domain] Cd Length: 216 Bit Score: 47.40 E-value: 4.20e-06
coenzyme PQQ biosynthesis enzyme PqqE; This model describes coenzyme PQQ biosynthesis protein ...
9-367
0e+00
coenzyme PQQ biosynthesis enzyme PqqE; This model describes coenzyme PQQ biosynthesis protein E, a prototypical peptide-cyclizing radical SAM enzyme. It links a Tyr to a Glu as the first step in the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ) from the precursor peptide PqqA. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
Pssm-ID: 162708 [Multi-domain] Cd Length: 358 Bit Score: 550.10 E-value: 0e+00
Iron-sulfur cluster-binding SPASM domain of coenzyme PQQ synthesis protein E; Coenzyme PQQ ...
240-349
1.16e-74
Iron-sulfur cluster-binding SPASM domain of coenzyme PQQ synthesis protein E; Coenzyme PQQ synthesis protein E (PqqE), also called pyrroloquinoline quinone (PQQ) biosynthesis protein E or PqqA peptide cyclase (EC 1.21.98.4), is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the formation of a C-C bond between C-4 of glutamate and C-3 of tyrosine residues of the PqqA protein, which is the first enzymatic step in the biosynthesis of the bacterial enzyme cofactor PQQ. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM (RS) enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. PqqE contains two auxiliary Fe-S clusters in its SPASM domain: one nearest the RS site (AuxI) is in the form of a 2Fe-2S cluster ligated by four cysteines; and a more remote cluster (AuxII) in the form of a 4Fe-4S center that is ligated by three cysteine residues and one aspartate residue.
Pssm-ID: 410610 [Multi-domain] Cd Length: 114 Bit Score: 226.80 E-value: 1.16e-74
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, ...
15-160
1.94e-43
Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, chromosome partitioning, Coenzyme transport and metabolism];
Pssm-ID: 440301 [Multi-domain] Cd Length: 159 Bit Score: 148.13 E-value: 1.94e-43
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
20-162
3.45e-18
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.
Pssm-ID: 427681 [Multi-domain] Cd Length: 159 Bit Score: 80.65 E-value: 3.45e-18
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in ...
19-334
6.65e-17
SynChlorMet cassette radical SAM/SPASM protein ScmE; A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Of the two PqqE homologs of the cassette, this family is the closer in sequence.
Pssm-ID: 211973 [Multi-domain] Cd Length: 358 Bit Score: 81.06 E-value: 6.65e-17
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
19-138
2.81e-15
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.
Pssm-ID: 100105 [Multi-domain] Cd Length: 204 Bit Score: 73.91 E-value: 2.81e-15
Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar ...
248-336
4.49e-15
Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar proteins; This group is composed of Mycobacterium tuberculosis putative mycofactocin radical SAM maturase MftC and similar proteins. MftC is a radical S-adenosylmethionine (SAM) enzyme that may function to modify mycofactocin, a conserved polypeptide that might serve as an electron carrier. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. This group appears to contain one auxillary Fe-S cluster that is similar to the second auxillary 4Fe-4S cluster (AuxII) of Clostridium perfringens anaerobic sulfatase-maturating enzyme (anSME).
Pssm-ID: 410614 [Multi-domain] Cd Length: 91 Bit Score: 69.98 E-value: 4.49e-15
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in ...
20-327
1.63e-13
SynChlorMet cassette radical SAM/SPASM protein ScmF; A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Of the two PqqE homologs of the cassette, this family is the more distant in sequence.
Pssm-ID: 211974 [Multi-domain] Cd Length: 353 Bit Score: 71.02 E-value: 1.63e-13
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and ...
20-185
3.55e-12
GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and metabolism]; GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) is part of the Pathway/BioSystem: Molybdopterin biosynthesis
Pssm-ID: 442141 [Multi-domain] Cd Length: 329 Bit Score: 66.62 E-value: 3.55e-12
Iron-sulfur cluster-binding domain; This domain occurs as an additional C-terminal iron-sulfur ...
243-309
3.41e-11
Iron-sulfur cluster-binding domain; This domain occurs as an additional C-terminal iron-sulfur cluster binding domain in many radical SAM domain, pfam04055 proteins. The domain occurs in a number of proteins that modify a protein to become an active enzyme, or a peptide to become a ribosomal natural product. The domain is named SPASM because it occurs in the maturases of Subilitosin, PQQ, Anaerobic Sulfatases, and Mycofactocin.
Pssm-ID: 433020 [Multi-domain] Cd Length: 66 Bit Score: 58.26 E-value: 3.41e-11
radical SAM additional 4Fe4S-binding SPASM domain; This domain contains regions binding ...
243-336
2.16e-09
radical SAM additional 4Fe4S-binding SPASM domain; This domain contains regions binding additional 4Fe4S clusters found in various radical SAM proteins C-terminal to the domain described by model pfam04055. Radical SAM enzymes with this domain tend to be involved in protein modification, including anaerobic sulfatase maturation proteins, a quinohemoprotein amine dehydrogenase biogenesis protein, the Pep1357-cyclizing radical SAM enzyme, and various bacteriocin biosynthesis proteins. The motif CxxCxxxxxCxxxC is nearly invariant for members of this family, although PqqE has a variant form. We name this domain SPASM for Subtilosin, PQQ, Anaerobic Sulfatase, and Mycofactocin.
Pssm-ID: 274968 [Multi-domain] Cd Length: 93 Bit Score: 54.12 E-value: 2.16e-09
Iron-sulfur cluster-binding SPASM domain; This iron-sulfur cluster-binding domain is named ...
243-308
5.40e-08
Iron-sulfur cluster-binding SPASM domain; This iron-sulfur cluster-binding domain is named SPASM after the biochemically characterized members, AlbA, PqqE, anSME, and MftC, which are involved in Subtilosin A, Pyrroloquinoline quinone, Anaerobic Sulfatase, and Mycofactocin maturation, respectively. SPASM occurs as an additional C-terminal domain in many peptide-modifying enzymes of the radical S-adenosylmethionine (SAM) superfamily. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster.
Pssm-ID: 410609 [Multi-domain] Cd Length: 65 Bit Score: 49.34 E-value: 5.40e-08
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
19-183
4.20e-06
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.
Pssm-ID: 214792 [Multi-domain] Cd Length: 216 Bit Score: 47.40 E-value: 4.20e-06
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic ...
24-97
9.95e-06
Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]; Organic radical activating enzyme NrdG/QueE is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440367 [Multi-domain] Cd Length: 205 Bit Score: 45.90 E-value: 9.95e-06
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of ...
24-116
1.30e-05
anaerobic ribonucleoside-triphosphate reductase activating protein; This enzyme is a member of the radical-SAM family (pfam04055). It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487) and presumably fulfills the identical function as NrdG, which utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in NrdD. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism, Protein fate, Protein modification and repair]
Pssm-ID: 274164 [Multi-domain] Cd Length: 192 Bit Score: 45.43 E-value: 1.30e-05
Iron-sulfur cluster-binding SPASM domain of antilisterial bacteriocin subtilosin biosynthesis ...
243-337
1.07e-04
Iron-sulfur cluster-binding SPASM domain of antilisterial bacteriocin subtilosin biosynthesis protein AlbA and similar proteins; Bacillus subtilis antilisterial bacteriocin subtilosin biosynthesis protein AlbA is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the formation of three thioether bonds in the post-translational modification of a linear peptide into the cyclic peptide subtilosin A. The thioether bonds formed are between the sulfur of three cysteine residues and the alpha-carbons of two phenylalanines and one threonine to produce a rigid cyclic peptide. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. AlbA appears to contain one auxillary Fe-S cluster, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN.
Pssm-ID: 410616 [Multi-domain] Cd Length: 97 Bit Score: 40.94 E-value: 1.07e-04
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to ...
24-89
5.64e-04
4Fe-4S single cluster domain; This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich.
Pssm-ID: 433138 [Multi-domain] Cd Length: 137 Bit Score: 39.85 E-value: 5.64e-04
Iron-sulfur cluster-binding SPASM domain of an uncharacterized group of radical SAM proteins; ...
243-306
7.69e-04
Iron-sulfur cluster-binding SPASM domain of an uncharacterized group of radical SAM proteins; Members of this group are radical S-adenosylmethionine (SAM) enzymes with a SPASM domain, named after the biochemically characterized members, AlbA, PqqE, anSME, and MftC, which are involved in Subtilosin A, Pyrroloquinoline quinone, Anaerobic Sulfatase, and Mycofactocin maturation, respectively. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. This group may contain one auxillary Fe-S cluster with an open coordination site, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN, but missing one conserved cysteine in the binding site.
Pssm-ID: 410619 [Multi-domain] Cd Length: 65 Bit Score: 37.35 E-value: 7.69e-04
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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