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Conserved domains on  [gi|108743072|emb|CAJ00493|]
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cobalamin-independent methionine synthase, partial [Saccharomyces bayanus x Saccharomyces cerevisiae x Saccharomyces kudriavzevii]

Protein Classification

uroporphyrinogen decarboxylase/cobalamine-independent methonine synthase family protein( domain architecture ID 1254)

uroporphyrinogen decarboxylase (URO-D)/cobalamine-independent methonine synthase (CIMS) family protein, similar to URO-D that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, an important branching point of the tetrapyrrole biosynthetic pathway

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
URO-D_CIMS_like super family cl00464
The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen ...
 1-138 4.20e-61

The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases. Despite their sequence similarities, members of this family have clearly different functions. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, an important branching point of the tetrapyrrole biosynthetic pathway. The methyltransferases represented here are important for ability of methanogenic organisms to use other compounds than carbon dioxide for reduction to methane, and methionine synthases transfer a methyl group from a folate cofactor to L-homocysteine in a reaction requiring zinc.


The actual alignment was detected with superfamily member cd03312:

Pssm-ID: 469779 [Multi-domain]  Cd Length: 360  Bit Score: 191.59  E-value: 4.20e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108743072   1 ILSKLAAAGATDVQIDEPVLVLDLPANAQAAIKKAYAYFGEQSNLPKITLATYFGTVVPNLDAIKGLPVAALHVDFVRAP 80
Cdd:cd03312  187 LLKKLAAAGAEWVQIDEPALVLDLPEEWLAAFKRAYEELAKAAPGLKLLLATYFGSLGENLDLLASLPVDGLHLDLVRGP 266

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 108743072  81 EQFDDVIAAIGAKQTLSVGIVDGRNIWKNDFKKSSAVVNKAIEKLGaDRVVVATSSSL 138
Cdd:cd03312  267 ENLEAVLKAGFADKVLSAGVVDGRNIWRADLAASLALLETLAAILG-DRLVVSPSCSL 323
 
Name Accession Description Interval E-value
CIMS_N_terminal_like cd03312
CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many ...
 1-138 4.20e-61

CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers the N-terminal barrel, and a few single-barrel sequences most similar to the N-terminal barrel. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Side chains from both barrels contribute to the binding of the folate substrate.


Pssm-ID: 239428 [Multi-domain]  Cd Length: 360  Bit Score: 191.59  E-value: 4.20e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108743072   1 ILSKLAAAGATDVQIDEPVLVLDLPANAQAAIKKAYAYFGEQSNLPKITLATYFGTVVPNLDAIKGLPVAALHVDFVRAP 80
Cdd:cd03312  187 LLKKLAAAGAEWVQIDEPALVLDLPEEWLAAFKRAYEELAKAAPGLKLLLATYFGSLGENLDLLASLPVDGLHLDLVRGP 266

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 108743072  81 EQFDDVIAAIGAKQTLSVGIVDGRNIWKNDFKKSSAVVNKAIEKLGaDRVVVATSSSL 138
Cdd:cd03312  267 ENLEAVLKAGFADKVLSAGVVDGRNIWRADLAASLALLETLAAILG-DRLVVSPSCSL 323
PRK05222 PRK05222
5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional
 1-138 1.57e-55

5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional


Pssm-ID: 235367 [Multi-domain]  Cd Length: 758  Bit Score: 184.55  E-value: 1.57e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108743072   1 ILSKLAAAGATDVQIDEPVLVLDLPANAQAAIKKAYAYFGEQSNLPKITLATYFGTVVPNLDAIKGLPVAALHVDFVRAP 80
Cdd:PRK05222 189 LLAELAAAGAEWVQIDEPALVLDLPQEWLEAFKRAYEALAAAKPRPKLLLATYFGSLNDALDLLASLPVDGLHLDLVRGP 268

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 108743072  81 EQFDDVIAAIGAKQTLSVGIVDGRNIWKNDFKKSSAVVNKAIEKlgADRVVVATSSSL 138
Cdd:PRK05222 269 EQLAALLKYFPADKVLSAGVIDGRNIWRADLEAALALLEPLAAK--VDRLWVAPSCSL 324
Meth_synt_1 pfam08267
Cobalamin-independent synthase, N-terminal domain; The N-terminal domain and C-terminal ...
 1-125 1.82e-51

Cobalamin-independent synthase, N-terminal domain; The N-terminal domain and C-terminal domains of cobalamin-independent synthases together define a catalytic cleft in the enzyme. The N-terminal domain is thought to bind the substrate, in particular, the negatively charged polyglutamate chain. The N-terminal domain is also thought to stabilize a loop from the C-terminal domain.


Pssm-ID: 400526 [Multi-domain]  Cd Length: 310  Bit Score: 165.45  E-value: 1.82e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108743072    1 ILSKLAAAGATDVQIDEPVLVLDLPANAQAAIKKAYAYFGEQSNLPKITLATYFGTVVPNLDAIKGLPVAALHVDFVRAP 80
Cdd:pfam08267 186 LLKELAAAGAEWVQIDEPALVLDLPPEWLAAFKEAYQELASAKPGPKLLLATYFGSVADALELLASLPVAGLGLDLVRGP 265

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 108743072   81 EQFDDVIAAIGAKQTLSVGIVDGRNIWKNDFKKSSAVVNKAIEKL 125
Cdd:pfam08267 266 ENLAALKKGFPADKVLSAGVIDGRNIWRADLEAALELLETLAQKL 310
MetE COG0620
Methionine synthase II (cobalamin-independent) [Amino acid transport and metabolism]; ...
 1-138 8.70e-36

Methionine synthase II (cobalamin-independent) [Amino acid transport and metabolism]; Methionine synthase II (cobalamin-independent) is part of the Pathway/BioSystem: Methionine biosynthesis


Pssm-ID: 440385 [Multi-domain]  Cd Length: 325  Bit Score: 125.25  E-value: 8.70e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108743072   1 ILSKLAAAGATDVQIDEPVLVLDLPANAQAAIKKAYAYFGEQSNLPKITLATYFGTVVPNLDAIKGLPVAALHVDFVRAP 80
Cdd:COG0620  159 ELKALEAAGARWIQIDEPALAEDLPDEYLDWAVEAYNRAAAGVPDTKIHLHTCYGGYEDILEALAALPVDGIHLEFVRSR 238

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 108743072  81 EQFDDVIAAIGAKQTLSVGIVDGRNIWKNDFKKSSAVVNKAIEKLGADRVVVATSSSL 138
Cdd:COG0620  239 AGLLEPLKELPYDKVLGLGVIDGRNPWVEDPEEVAARIEEALKYVPPERLWVSPDCGL 296
 
Name Accession Description Interval E-value
CIMS_N_terminal_like cd03312
CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many ...
 1-138 4.20e-61

CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers the N-terminal barrel, and a few single-barrel sequences most similar to the N-terminal barrel. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Side chains from both barrels contribute to the binding of the folate substrate.


Pssm-ID: 239428 [Multi-domain]  Cd Length: 360  Bit Score: 191.59  E-value: 4.20e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108743072   1 ILSKLAAAGATDVQIDEPVLVLDLPANAQAAIKKAYAYFGEQSNLPKITLATYFGTVVPNLDAIKGLPVAALHVDFVRAP 80
Cdd:cd03312  187 LLKKLAAAGAEWVQIDEPALVLDLPEEWLAAFKRAYEELAKAAPGLKLLLATYFGSLGENLDLLASLPVDGLHLDLVRGP 266

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 108743072  81 EQFDDVIAAIGAKQTLSVGIVDGRNIWKNDFKKSSAVVNKAIEKLGaDRVVVATSSSL 138
Cdd:cd03312  267 ENLEAVLKAGFADKVLSAGVVDGRNIWRADLAASLALLETLAAILG-DRLVVSPSCSL 323
PRK05222 PRK05222
5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional
 1-138 1.57e-55

5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional


Pssm-ID: 235367 [Multi-domain]  Cd Length: 758  Bit Score: 184.55  E-value: 1.57e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108743072   1 ILSKLAAAGATDVQIDEPVLVLDLPANAQAAIKKAYAYFGEQSNLPKITLATYFGTVVPNLDAIKGLPVAALHVDFVRAP 80
Cdd:PRK05222 189 LLAELAAAGAEWVQIDEPALVLDLPQEWLEAFKRAYEALAAAKPRPKLLLATYFGSLNDALDLLASLPVDGLHLDLVRGP 268

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 108743072  81 EQFDDVIAAIGAKQTLSVGIVDGRNIWKNDFKKSSAVVNKAIEKlgADRVVVATSSSL 138
Cdd:PRK05222 269 EQLAALLKYFPADKVLSAGVIDGRNIWRADLEAALALLEPLAAK--VDRLWVAPSCSL 324
Meth_synt_1 pfam08267
Cobalamin-independent synthase, N-terminal domain; The N-terminal domain and C-terminal ...
 1-125 1.82e-51

Cobalamin-independent synthase, N-terminal domain; The N-terminal domain and C-terminal domains of cobalamin-independent synthases together define a catalytic cleft in the enzyme. The N-terminal domain is thought to bind the substrate, in particular, the negatively charged polyglutamate chain. The N-terminal domain is also thought to stabilize a loop from the C-terminal domain.


Pssm-ID: 400526 [Multi-domain]  Cd Length: 310  Bit Score: 165.45  E-value: 1.82e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108743072    1 ILSKLAAAGATDVQIDEPVLVLDLPANAQAAIKKAYAYFGEQSNLPKITLATYFGTVVPNLDAIKGLPVAALHVDFVRAP 80
Cdd:pfam08267 186 LLKELAAAGAEWVQIDEPALVLDLPPEWLAAFKEAYQELASAKPGPKLLLATYFGSVADALELLASLPVAGLGLDLVRGP 265

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 108743072   81 EQFDDVIAAIGAKQTLSVGIVDGRNIWKNDFKKSSAVVNKAIEKL 125
Cdd:pfam08267 266 ENLAALKKGFPADKVLSAGVIDGRNIWRADLEAALELLETLAQKL 310
MetE COG0620
Methionine synthase II (cobalamin-independent) [Amino acid transport and metabolism]; ...
 1-138 8.70e-36

Methionine synthase II (cobalamin-independent) [Amino acid transport and metabolism]; Methionine synthase II (cobalamin-independent) is part of the Pathway/BioSystem: Methionine biosynthesis


Pssm-ID: 440385 [Multi-domain]  Cd Length: 325  Bit Score: 125.25  E-value: 8.70e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108743072   1 ILSKLAAAGATDVQIDEPVLVLDLPANAQAAIKKAYAYFGEQSNLPKITLATYFGTVVPNLDAIKGLPVAALHVDFVRAP 80
Cdd:COG0620  159 ELKALEAAGARWIQIDEPALAEDLPDEYLDWAVEAYNRAAAGVPDTKIHLHTCYGGYEDILEALAALPVDGIHLEFVRSR 238

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 108743072  81 EQFDDVIAAIGAKQTLSVGIVDGRNIWKNDFKKSSAVVNKAIEKLGADRVVVATSSSL 138
Cdd:COG0620  239 AGLLEPLKELPYDKVLGLGVIDGRNPWVEDPEEVAARIEEALKYVPPERLWVSPDCGL 296
PLN02475 PLN02475
5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
 1-138 9.09e-27

5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase


Pssm-ID: 215264 [Multi-domain]  Cd Length: 766  Bit Score: 104.09  E-value: 9.09e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108743072   1 ILSKLAAAGATDVQIDEPVLVLDLPANAQAAIKKAYAYFGEQSNLPKITLATYFGTV-VPNLDAIKGLP-VAALHVDFVR 78
Cdd:PLN02475 191 VIAELKAAGASWIQFDEPALVMDLESHKLQAFKTAYAELESTLSGLNVLVETYFADVpAEAYKTLTSLKgVTAFGFDLVR 270

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 108743072  79 aPEQFDDVIAAIG--AKQTLSVGIVDGRNIWKNDFKKSSAVVNKAIEKLGADRVVVATSSSL 138
Cdd:PLN02475 271 -GTKTLDLIKKAGfpSGKYLFAGVVDGRNIWANDLAASLATLQALEGIVGKDKLVVSTSCSL 331
CIMS_like cd03310
CIMS - Cobalamine-independent methonine synthase, or MetE. Many members have been ...
 2-136 2.36e-04

CIMS - Cobalamine-independent methonine synthase, or MetE. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers both the N-and C-terminal barrel, and some single-barrel sequences, mostly from Archaea. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Side chains from both barrels contribute to the binding of the folate substrate.


Pssm-ID: 239426 [Multi-domain]  Cd Length: 321  Bit Score: 39.33  E-value: 2.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108743072   2 LSKLAAAGATDVQIDEPVLVLDLPA--NAQAAIKKAYAYFGEQSNLPKiTLATYFGTVvpnLDAIKGLPVAALHVDFVRA 79
Cdd:cd03310  157 VKELKNRGIVVVQIDEPSLGAVGAGafEDLEIVDAALEEVSLKSGGDV-EVHLCAPLD---YEALLELGVDVIGFDAAAL 232

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 108743072  80 PEQFDDVIAAIGAKQ--TLSVGIVDGRNIWKN-DFKKSSAVVNKAIEKLGADRVVVATSS 136
Cdd:cd03310  233 PSKYLEDLKKLLRIGvrTLILGLVVTDNEAKGrNAWKEIERLEKLVRRLEEPGEVLDEIL 292
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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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