NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1602591412|emb|VGH63874|]
View 

pyruvate formate-lyase [Klebsiella pneumoniae]

Protein Classification

autonomous glycyl radical cofactor GrcA( domain architecture ID 10013746)

autonomous glycyl radical cofactor GrcA is similar to pyruvate formate-lyase-activating protein and may act as a radical domain for damaged PFL or other radical proteins

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK11127 PRK11127
autonomous glycyl radical cofactor GrcA; Provisional
 1-127 7.78e-97

autonomous glycyl radical cofactor GrcA; Provisional


:

Pssm-ID: 182983 [Multi-domain]  Cd Length: 127  Bit Score: 273.64  E-value: 7.78e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1602591412   1 MITGIQITKAANDDLLNSFWLLDSEKGEARCLCAKGGFAEDDVVAVSKLGEIEYREIPVDVKPEVRVEGGQHLNVNVLRR 80
Cdd:PRK11127    1 MITGIQITKAANDDLLNSFWLLDSEKGEARCIVAKAGYAEDQVVAVSKLGEIEYREVPVEVKPEVRVEGGQHLNVNVLRR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1602591412  81 ETLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTESL 127
Cdd:PRK11127   81 ETLEDAVKHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTESL 127
 
Name Accession Description Interval E-value
PRK11127 PRK11127
autonomous glycyl radical cofactor GrcA; Provisional
 1-127 7.78e-97

autonomous glycyl radical cofactor GrcA; Provisional


Pssm-ID: 182983 [Multi-domain]  Cd Length: 127  Bit Score: 273.64  E-value: 7.78e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1602591412   1 MITGIQITKAANDDLLNSFWLLDSEKGEARCLCAKGGFAEDDVVAVSKLGEIEYREIPVDVKPEVRVEGGQHLNVNVLRR 80
Cdd:PRK11127    1 MITGIQITKAANDDLLNSFWLLDSEKGEARCIVAKAGYAEDQVVAVSKLGEIEYREVPVEVKPEVRVEGGQHLNVNVLRR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1602591412  81 ETLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTESL 127
Cdd:PRK11127   81 ETLEDAVKHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTESL 127
GrcA COG3445
Autonomous glycyl radical cofactor GrcA [Coenzyme transport and metabolism];
1-127 1.35e-91

Autonomous glycyl radical cofactor GrcA [Coenzyme transport and metabolism];


Pssm-ID: 442669 [Multi-domain]  Cd Length: 125  Bit Score: 260.44  E-value: 1.35e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1602591412   1 MITGIQITKAANDDLLNSFWLLDSEKGEARCLCAKGGFAEDDVVAVSKLGEIEYREIPVDVKPevRVEGGQHLNVNVLRR 80
Cdd:COG3445     1 MIKGIQITKSANAALLNSFWLLDEEKNEARCLCAKDDYAEDQVVALAELGQFEYREVPVEAPP--RVEGGQHLNVNVLRR 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1602591412  81 ETLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTESL 127
Cdd:COG3445    79 ETLEDAVKHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVITRTFTESL 125
spare_glycyl TIGR04365
autonomous glycyl radical cofactor GrcA; This small protein, previously designated YfiD in E. ...
 2-127 5.78e-83

autonomous glycyl radical cofactor GrcA; This small protein, previously designated YfiD in E. coli, is closely homologous to pyruvate formate_lyase (PFL) in a region surrounding the stable glycyl radical that is prepared by the action of pyruvate formate-lyase activase, a radical SAM enzyme. When damage at the site of this radical breaks the main chain of PFL, this protein acts as a spare part that reintroduces the needed stable glycyl radical. Cutoffs for this model are set to exclude a set of closely related phage proteins that appear to have a corresponding function.


Pssm-ID: 213978 [Multi-domain]  Cd Length: 124  Bit Score: 238.55  E-value: 5.78e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1602591412   2 ITGIQITKAANDDLLNSFWLLDSEKGEARCLCAKGGFAEDDVVAVSKLGEIEYREIPVDVKPevRVEGGQHLNVNVLRRE 81
Cdd:TIGR04365   1 IKGIQITKAANQALLNSFWLLDEETNQARCLVAKAGFAADQVVPLSELGDFEYREIAIEAPA--KVEGGQHLNVNVLTRE 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1602591412  82 TLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTESL 127
Cdd:TIGR04365  79 TLEDAVKNPEKYPQLTIRVSGYAVRFNSLTPEQQRDVITRTFTESL 124
rad_fix_GrcA3 NF038360
autonomous glycyl radical cofactor GrcA3; This small protein, like GrcA and GrcA2, is a ...
 68-127 5.87e-35

autonomous glycyl radical cofactor GrcA3; This small protein, like GrcA and GrcA2, is a lineage-specific small protein related to the glycyl radical active site-containing C-terminal region of pyruvate formate-lyase (PFL, also called formate C-acetyltransferase) from similar species. Because PFL is prone to damage and inactivation, this protein is made as a spare part that fills in for the portion of the protein that was damaged and lost. The distinct families we now call GrcA, GrcA2, and GrcA3 all have the surprising property of being much more closely related to some full length PFL than to members of the other GrcA-series families.


Pssm-ID: 439653 [Multi-domain]  Cd Length: 78  Bit Score: 115.61  E-value: 5.87e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1602591412  68 EGGQHLNVNVLRRETLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTESL 127
Cdd:NF038360   19 KGGHHLNVNVFNRETLLDAQAHPEKYPQLTVRVSGYAVNFNKLTKEQQDEVISRTFHEAM 78
PFL1 cd01678
Pyruvate formate lyase 1; Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, ...
 69-123 3.24e-33

Pyruvate formate lyase 1; Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, the conversion of pyruvate and CoenzymeA to formate and acetylCoA. The PFL mechanism involves an unusual radical cleavage of pyruvate in which two cysteines and one glycine form radicals that are required for catalysis. PFL has a ten-stranded alpha/beta barrel domain that is structurally similar to those of all three ribonucleotide reductase (RNR) classes as well as benzylsuccinate synthase and B12-independent glycerol dehydratase.


Pssm-ID: 153087 [Multi-domain]  Cd Length: 738  Bit Score: 121.70  E-value: 3.24e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1602591412  69 GGQHLNVNVLRRETLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTF 123
Cdd:cd01678   683 GGHHLNVNVLNRETLLDAMEHPEKYPQLTIRVSGYAVNFVKLTREQQLDVISRTF 737
Gly_radical pfam01228
Glycine radical;
42-108 4.97e-26

Glycine radical;


Pssm-ID: 426140 [Multi-domain]  Cd Length: 106  Bit Score: 93.77  E-value: 4.97e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1602591412  42 DVVAVSKLGEIEYREIPVDVKpevrVEGGQHLNVNVLRRETLLDAVEHPEKYPQLTIRVSGYAVRFN 108
Cdd:pfam01228  44 AVLGYYDEEGYANLNTLIDTY----FEGGHHLQFNVVDRETLPDAQKHPEKYPDLTVRVSGYSANFV 106
 
Name Accession Description Interval E-value
PRK11127 PRK11127
autonomous glycyl radical cofactor GrcA; Provisional
 1-127 7.78e-97

autonomous glycyl radical cofactor GrcA; Provisional


Pssm-ID: 182983 [Multi-domain]  Cd Length: 127  Bit Score: 273.64  E-value: 7.78e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1602591412   1 MITGIQITKAANDDLLNSFWLLDSEKGEARCLCAKGGFAEDDVVAVSKLGEIEYREIPVDVKPEVRVEGGQHLNVNVLRR 80
Cdd:PRK11127    1 MITGIQITKAANDDLLNSFWLLDSEKGEARCIVAKAGYAEDQVVAVSKLGEIEYREVPVEVKPEVRVEGGQHLNVNVLRR 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1602591412  81 ETLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTESL 127
Cdd:PRK11127   81 ETLEDAVKHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTESL 127
GrcA COG3445
Autonomous glycyl radical cofactor GrcA [Coenzyme transport and metabolism];
1-127 1.35e-91

Autonomous glycyl radical cofactor GrcA [Coenzyme transport and metabolism];


Pssm-ID: 442669 [Multi-domain]  Cd Length: 125  Bit Score: 260.44  E-value: 1.35e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1602591412   1 MITGIQITKAANDDLLNSFWLLDSEKGEARCLCAKGGFAEDDVVAVSKLGEIEYREIPVDVKPevRVEGGQHLNVNVLRR 80
Cdd:COG3445     1 MIKGIQITKSANAALLNSFWLLDEEKNEARCLCAKDDYAEDQVVALAELGQFEYREVPVEAPP--RVEGGQHLNVNVLRR 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1602591412  81 ETLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTESL 127
Cdd:COG3445    79 ETLEDAVKHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVITRTFTESL 125
spare_glycyl TIGR04365
autonomous glycyl radical cofactor GrcA; This small protein, previously designated YfiD in E. ...
 2-127 5.78e-83

autonomous glycyl radical cofactor GrcA; This small protein, previously designated YfiD in E. coli, is closely homologous to pyruvate formate_lyase (PFL) in a region surrounding the stable glycyl radical that is prepared by the action of pyruvate formate-lyase activase, a radical SAM enzyme. When damage at the site of this radical breaks the main chain of PFL, this protein acts as a spare part that reintroduces the needed stable glycyl radical. Cutoffs for this model are set to exclude a set of closely related phage proteins that appear to have a corresponding function.


Pssm-ID: 213978 [Multi-domain]  Cd Length: 124  Bit Score: 238.55  E-value: 5.78e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1602591412   2 ITGIQITKAANDDLLNSFWLLDSEKGEARCLCAKGGFAEDDVVAVSKLGEIEYREIPVDVKPevRVEGGQHLNVNVLRRE 81
Cdd:TIGR04365   1 IKGIQITKAANQALLNSFWLLDEETNQARCLVAKAGFAADQVVPLSELGDFEYREIAIEAPA--KVEGGQHLNVNVLTRE 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1602591412  82 TLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTESL 127
Cdd:TIGR04365  79 TLEDAVKNPEKYPQLTIRVSGYAVRFNSLTPEQQRDVITRTFTESL 124
rad_fix_GrcA3 NF038360
autonomous glycyl radical cofactor GrcA3; This small protein, like GrcA and GrcA2, is a ...
 68-127 5.87e-35

autonomous glycyl radical cofactor GrcA3; This small protein, like GrcA and GrcA2, is a lineage-specific small protein related to the glycyl radical active site-containing C-terminal region of pyruvate formate-lyase (PFL, also called formate C-acetyltransferase) from similar species. Because PFL is prone to damage and inactivation, this protein is made as a spare part that fills in for the portion of the protein that was damaged and lost. The distinct families we now call GrcA, GrcA2, and GrcA3 all have the surprising property of being much more closely related to some full length PFL than to members of the other GrcA-series families.


Pssm-ID: 439653 [Multi-domain]  Cd Length: 78  Bit Score: 115.61  E-value: 5.87e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1602591412  68 EGGQHLNVNVLRRETLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTESL 127
Cdd:NF038360   19 KGGHHLNVNVFNRETLLDAQAHPEKYPQLTVRVSGYAVNFNKLTKEQQDEVISRTFHEAM 78
PFL1 cd01678
Pyruvate formate lyase 1; Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, ...
 69-123 3.24e-33

Pyruvate formate lyase 1; Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, the conversion of pyruvate and CoenzymeA to formate and acetylCoA. The PFL mechanism involves an unusual radical cleavage of pyruvate in which two cysteines and one glycine form radicals that are required for catalysis. PFL has a ten-stranded alpha/beta barrel domain that is structurally similar to those of all three ribonucleotide reductase (RNR) classes as well as benzylsuccinate synthase and B12-independent glycerol dehydratase.


Pssm-ID: 153087 [Multi-domain]  Cd Length: 738  Bit Score: 121.70  E-value: 3.24e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1602591412  69 GGQHLNVNVLRRETLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTF 123
Cdd:cd01678   683 GGHHLNVNVLNRETLLDAMEHPEKYPQLTIRVSGYAVNFVKLTREQQLDVISRTF 737
PflD COG1882
Pyruvate-formate lyase [Energy production and conversion]; Pyruvate-formate lyase is part of ...
 69-126 9.96e-33

Pyruvate-formate lyase [Energy production and conversion]; Pyruvate-formate lyase is part of the Pathway/BioSystem: Pyruvate oxidation


Pssm-ID: 441486 [Multi-domain]  Cd Length: 789  Bit Score: 120.65  E-value: 9.96e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1602591412  69 GGQHLNVNVLRRETLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTES 126
Cdd:COG1882   732 GGHHIQFNVVDRETLLDAQKHPEKYPDLTVRVAGYSAYFVELSKEQQDDIIARTEHEF 789
Gly_radical pfam01228
Glycine radical;
42-108 4.97e-26

Glycine radical;


Pssm-ID: 426140 [Multi-domain]  Cd Length: 106  Bit Score: 93.77  E-value: 4.97e-26
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1602591412  42 DVVAVSKLGEIEYREIPVDVKpevrVEGGQHLNVNVLRRETLLDAVEHPEKYPQLTIRVSGYAVRFN 108
Cdd:pfam01228  44 AVLGYYDEEGYANLNTLIDTY----FEGGHHLQFNVVDRETLPDAQKHPEKYPDLTVRVSGYSANFV 106
PFL2_DhaB_BssA cd01677
Pyruvate formate lyase 2 and related enzymes; This family includes pyruvate formate lyase 2 ...
 69-122 6.66e-16

Pyruvate formate lyase 2 and related enzymes; This family includes pyruvate formate lyase 2 (PFL2), B12-independent glycerol dehydratase (DhaB) and the alpha subunit of benzylsuccinate synthase (BssA), all of which have a highly conserved ten-stranded alpha/beta barrel domain, which is similar to those of PFL1 (pyruvate formate lyase 1) and RNR (ribonucleotide reductase). Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, the conversion of pyruvate and CoenzymeA to formate and acetylCoA. DhaB catalyzes the first step in the conversion of glycerol to 1,3-propanediol while BssA catalyzes the first step in the anaerobic mineralization of both toluene and m-xylene.


Pssm-ID: 153086 [Multi-domain]  Cd Length: 781  Bit Score: 72.31  E-value: 6.66e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1602591412  69 GGQHLNVNVLRRETLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIART 122
Cdd:cd01677   727 GGHHIQFNVVSAETLRDAQKHPEKYRDLIVRVAGYSAYFVELSKEVQDEIIART 780
pflD PRK09983
putative formate acetyltransferase 2; Provisional
 71-122 6.46e-11

putative formate acetyltransferase 2; Provisional


Pssm-ID: 182181 [Multi-domain]  Cd Length: 765  Bit Score: 58.29  E-value: 6.46e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1602591412  71 QHLNVNVLRRETLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIART 122
Cdd:PRK09983  710 QHIQFNVVNADTLREAQQRPQDYAGLVVRVAGYSAFFVELSKEIQDDIIRRT 761
choline_CutC TIGR04394
choline trimethylamine-lyase; Members of this family, homologs to pyruvate formate-lyases and ...
 69-125 4.97e-10

choline trimethylamine-lyase; Members of this family, homologs to pyruvate formate-lyases and benzylsuccinate synthases, are glycine radical enzymes that appear to act as choline TMA-lyase, that is, to perform a C-N bond cleavage turning choline into trimethylamine (TMA) plus acetaldehyde. The gene symbol is cutC, for choline utilization. The activase, CutD, is a radical SAM enzyme. [Energy metabolism, Amino acids and amines]


Pssm-ID: 275187 [Multi-domain]  Cd Length: 789  Bit Score: 55.58  E-value: 4.97e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1602591412  69 GGQHLNVNVLRRETLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTE 125
Cdd:TIGR04394 731 GNGEMQFNYLDNETLLDAQQHPEKYRDLVVRVAGYSAFFVELCKDVQDEIISRTMLE 787
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH