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Conserved domains on  [gi|1289857924|gb|PJX34069|]
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6-carboxytetrahydropterin synthase QueD [Klebsiella sp. A-Nf5]

Protein Classification

tunnelling fold family protein( domain architecture ID 365)

Tunnelling fold (T-fold) family protein such as dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl tetrahydropterin synthetase (PTPS), and uricase (UO,uroate/urate oxidase)

PubMed:  10737935
SCOP:  3000283

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TFold super family cl00263
Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with ...
 2-120 1.33e-58

Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl tetrahydropterin synthetase (PTPS), and uricase (UO,uroate/urate oxidase). They bind to substrates belonging to the purine or pterin families, and share a fold-related binding site with a glutamate or glutamine residue anchoring the substrate and a lot of conserved interactions. They also share a similar oligomerization mode: several T-folds join together to form a beta(2n)alpha(n) barrel, then two barrels join together in a head-to-head fashion to made up the native enzymes. The functional enzyme is a tetramer for UO, a hexamer for PTPS, an octamer for DHNA/DHNTPE and a decamer for GTPCH-1. The substrate is located in a deep and narrow pocket at the interface between monomers. In PTPS, the active site is located at the interface of three monomers, two from one trimer and one from the other trimer. In GTPCH-1, it is also located at the interface of three subunits, two from one pentamer and one from the other pentamer. There are four equivalent active sites in UO, six in PTPS, eight in DHNA/DHNTPE and ten in GTPCH-1. Each globular multimeric enzyme encloses a tunnel which is lined with charged residues for DHNA and UO, and with basic residues in PTPS. The N and C-terminal ends are located on one side of the T-fold while the residues involved in the catalytic activity are located at the opposite side. In PTPS, UO and DHNA/DHNTPE, the N and C-terminal extremities of the enzyme are located on the exterior side of the functional multimeric enzyme. In GTPCH-1, the extra C-terminal helix places the extremity inside the tunnel.


The actual alignment was detected with superfamily member cd00470:

Pssm-ID: 469697  Cd Length: 135  Bit Score: 177.04  E-value: 1.33e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1289857924   2 STTLFKDFTFEAAHHLPHVP--------EGHKCG--RLHGHSFMVRLEITGEVDPHTGWIMDFAELK-AAFKPTYDRLDH 70
Cdd:cd00470     1 SATLTRRFSFSACHRLHSPPlsdeenleVFGKCNnpNGHGHNYKVEVTVRGEIDPVTGMVMNLTDLKkAIEEAIMKPLDH 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1289857924  71 YYLNDIPG---LENPTSEVLAKWIWDEMKPRVP--LLSAVMVKETCTAGCIYRGE 120
Cdd:cd00470    81 KNLDDDVPyfaDVVSTTENLAVYIWDNLQKVLPvgLLYEVKVHETDKNIVVYRGE 135
 
Name Accession Description Interval E-value
PTPS cd00470
6-pyruvoyl tetrahydropterin synthase (PTPS). Folate derivatives are essential cofactors in the ...
 2-120 1.33e-58

6-pyruvoyl tetrahydropterin synthase (PTPS). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids, as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after uptake by a carrier-mediated active transport system. Most microbes and plants lack this system and must synthesize folates de novo from guanosine triphosphate. One enzyme from this pathway is PTPS which catalyzes the conversion of dihydroneopterin triphosphate to 6-pyruvoyl tetrahydropterin. The functional enzyme is a hexamer of identical subunits.


Pssm-ID: 238264  Cd Length: 135  Bit Score: 177.04  E-value: 1.33e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1289857924   2 STTLFKDFTFEAAHHLPHVP--------EGHKCG--RLHGHSFMVRLEITGEVDPHTGWIMDFAELK-AAFKPTYDRLDH 70
Cdd:cd00470     1 SATLTRRFSFSACHRLHSPPlsdeenleVFGKCNnpNGHGHNYKVEVTVRGEIDPVTGMVMNLTDLKkAIEEAIMKPLDH 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1289857924  71 YYLNDIPG---LENPTSEVLAKWIWDEMKPRVP--LLSAVMVKETCTAGCIYRGE 120
Cdd:cd00470    81 KNLDDDVPyfaDVVSTTENLAVYIWDNLQKVLPvgLLYEVKVHETDKNIVVYRGE 135
QueD COG0720
6-pyruvoyl-tetrahydropterin synthase [Coenzyme transport and metabolism]; ...
 4-120 1.95e-53

6-pyruvoyl-tetrahydropterin synthase [Coenzyme transport and metabolism]; 6-pyruvoyl-tetrahydropterin synthase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440484  Cd Length: 123  Bit Score: 163.45  E-value: 1.95e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1289857924   4 TLFKDFTFEAAHHLPHVpeGHKCGRLHGHSFMVRLEITGEVDPHTGWIMDFAELKAAFKPTYDRLDHYYLNDIPGLE--N 81
Cdd:COG0720     3 RITKEFRFSAAHRLPGH--DGKCGRLHGHNYRVEVTVEGEELDETGMVVDFGDLKAALKEVIDRLDHRFLNELPDLEglN 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1289857924  82 PTSEVLAKWIWDEMKPRVPL---LSAVMVKETCTAGCIYRGE 120
Cdd:COG0720    81 PTAENLARWIWDRLAPRLPGgvrLLRVRVYETPTNWAEYEGE 122
6PTHBS TIGR00039
6-pyruvoyl tetrahydropterin synthase/QueD family protein; This model has been downgraded from ...
 2-120 2.95e-47

6-pyruvoyl tetrahydropterin synthase/QueD family protein; This model has been downgraded from hypothetical_equivalog to subfamily. The animal enzymes are known to be 6-pyruvoyl tetrahydropterin synthase. The function of the bacterial branch of the sequence lineage had been thought to be the same, but many are now taken to be QueD, and enzyme of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of some tRNAs in most species. A new model is built to be the QueD equivalog model. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 272868  Cd Length: 124  Bit Score: 147.89  E-value: 2.95e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1289857924   2 STTLFKDFTFEAAHHLPHVPEghKCGRLHGHSFMVRLEITGEVDPHTGWIMDFAELKAAFKPTYDR-LDHYYLNDIPG-L 79
Cdd:TIGR00039   1 MFGIHKEFSFSAAHRLPGHEG--KCGNLHGHSYKVDVEVSGERDPKTGMVMDFSDLKKIVKEVIDEpLDHKLLNDDVNyL 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1289857924  80 ENPTSEVLAKWIWDEMKPR-VPLLSAVMVKETCTAG--CIYRGE 120
Cdd:TIGR00039  79 ENPTSENVAVYIFDNLKEYlIPVENLVKVKEEETPAeiRIYRGP 122
PTPS pfam01242
6-pyruvoyl tetrahydropterin synthase; 6-Pyruvoyl tetrahydrobiopterin synthase catalyzes the ...
 4-120 5.80e-46

6-pyruvoyl tetrahydropterin synthase; 6-Pyruvoyl tetrahydrobiopterin synthase catalyzes the conversion of dihydroneopterin triphosphate to 6-pyruvoyl tetrahydropterin, the second of three enzymatic steps in the synthesis of tetrahydrobiopterin from GTP. The functional enzyme is a hexamer of identical subunits.


Pssm-ID: 460129  Cd Length: 121  Bit Score: 144.26  E-value: 5.80e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1289857924   4 TLFKDFTFEAAHHLPHVPegHKCGRLHGHSFMVRLEITGEVDPHTGWIMDFAELKAAFKPTYDRLDHYYLNDIPGLE--N 81
Cdd:pfam01242   1 EITKEFRFDAAHRLPDYP--GKCSNLHGHNYRVEVTVRGEELDETGMVVDFGELKKAVKEVLDRLDHRFLNDDPEFEtlN 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1289857924  82 PTSEVLAKWIWDEMKPRV----PLLSAVMVKETCTAGCIYRGE 120
Cdd:pfam01242  79 PTAENLARYIFERLKPRLsgggVRLARVRVWETPTSWAEYRGE 121
 
Name Accession Description Interval E-value
PTPS cd00470
6-pyruvoyl tetrahydropterin synthase (PTPS). Folate derivatives are essential cofactors in the ...
 2-120 1.33e-58

6-pyruvoyl tetrahydropterin synthase (PTPS). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids, as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after uptake by a carrier-mediated active transport system. Most microbes and plants lack this system and must synthesize folates de novo from guanosine triphosphate. One enzyme from this pathway is PTPS which catalyzes the conversion of dihydroneopterin triphosphate to 6-pyruvoyl tetrahydropterin. The functional enzyme is a hexamer of identical subunits.


Pssm-ID: 238264  Cd Length: 135  Bit Score: 177.04  E-value: 1.33e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1289857924   2 STTLFKDFTFEAAHHLPHVP--------EGHKCG--RLHGHSFMVRLEITGEVDPHTGWIMDFAELK-AAFKPTYDRLDH 70
Cdd:cd00470     1 SATLTRRFSFSACHRLHSPPlsdeenleVFGKCNnpNGHGHNYKVEVTVRGEIDPVTGMVMNLTDLKkAIEEAIMKPLDH 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1289857924  71 YYLNDIPG---LENPTSEVLAKWIWDEMKPRVP--LLSAVMVKETCTAGCIYRGE 120
Cdd:cd00470    81 KNLDDDVPyfaDVVSTTENLAVYIWDNLQKVLPvgLLYEVKVHETDKNIVVYRGE 135
QueD COG0720
6-pyruvoyl-tetrahydropterin synthase [Coenzyme transport and metabolism]; ...
 4-120 1.95e-53

6-pyruvoyl-tetrahydropterin synthase [Coenzyme transport and metabolism]; 6-pyruvoyl-tetrahydropterin synthase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440484  Cd Length: 123  Bit Score: 163.45  E-value: 1.95e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1289857924   4 TLFKDFTFEAAHHLPHVpeGHKCGRLHGHSFMVRLEITGEVDPHTGWIMDFAELKAAFKPTYDRLDHYYLNDIPGLE--N 81
Cdd:COG0720     3 RITKEFRFSAAHRLPGH--DGKCGRLHGHNYRVEVTVEGEELDETGMVVDFGDLKAALKEVIDRLDHRFLNELPDLEglN 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1289857924  82 PTSEVLAKWIWDEMKPRVPL---LSAVMVKETCTAGCIYRGE 120
Cdd:COG0720    81 PTAENLARWIWDRLAPRLPGgvrLLRVRVYETPTNWAEYEGE 122
6PTHBS TIGR00039
6-pyruvoyl tetrahydropterin synthase/QueD family protein; This model has been downgraded from ...
 2-120 2.95e-47

6-pyruvoyl tetrahydropterin synthase/QueD family protein; This model has been downgraded from hypothetical_equivalog to subfamily. The animal enzymes are known to be 6-pyruvoyl tetrahydropterin synthase. The function of the bacterial branch of the sequence lineage had been thought to be the same, but many are now taken to be QueD, and enzyme of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of some tRNAs in most species. A new model is built to be the QueD equivalog model. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 272868  Cd Length: 124  Bit Score: 147.89  E-value: 2.95e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1289857924   2 STTLFKDFTFEAAHHLPHVPEghKCGRLHGHSFMVRLEITGEVDPHTGWIMDFAELKAAFKPTYDR-LDHYYLNDIPG-L 79
Cdd:TIGR00039   1 MFGIHKEFSFSAAHRLPGHEG--KCGNLHGHSYKVDVEVSGERDPKTGMVMDFSDLKKIVKEVIDEpLDHKLLNDDVNyL 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1289857924  80 ENPTSEVLAKWIWDEMKPR-VPLLSAVMVKETCTAG--CIYRGE 120
Cdd:TIGR00039  79 ENPTSENVAVYIFDNLKEYlIPVENLVKVKEEETPAeiRIYRGP 122
queuosine_QueD TIGR03367
queuosine biosynthesis protein QueD; Members of this protein family, closely related to ...
 5-95 9.17e-47

queuosine biosynthesis protein QueD; Members of this protein family, closely related to eukaryotic 6-pyruvoyl tetrahydrobiopterin synthase enzymes, are the QueD protein of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of tRNAs for Tyr, His, Asp, and Asn in many species. This modification, although widespread, appears not to be important for viability. The queuosine precursor made by this enzyme may be converted instead to archeaosine as in some Archaea. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 274547  Cd Length: 89  Bit Score: 145.42  E-value: 9.17e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1289857924   5 LFKDFTFEAAHHLPHVPEghKCGRLHGHSFMVRLEITGEVDPHTGWIMDFAELKAAFKPTYDRLDHYYLNDIPGLENPTS 84
Cdd:TIGR03367   1 ITKEFTFDAAHRLPGYPG--KCARLHGHTYKVEVTVSGEVLDEAGMVMDFSDLKAIVKEVVDRLDHALLNDVLGLENPTA 78

                          90
                  ....*....|.
gi 1289857924  85 EVLAKWIWDEM 95
Cdd:TIGR03367  79 ENLARWIYDRL 89
PTPS pfam01242
6-pyruvoyl tetrahydropterin synthase; 6-Pyruvoyl tetrahydrobiopterin synthase catalyzes the ...
 4-120 5.80e-46

6-pyruvoyl tetrahydropterin synthase; 6-Pyruvoyl tetrahydrobiopterin synthase catalyzes the conversion of dihydroneopterin triphosphate to 6-pyruvoyl tetrahydropterin, the second of three enzymatic steps in the synthesis of tetrahydrobiopterin from GTP. The functional enzyme is a hexamer of identical subunits.


Pssm-ID: 460129  Cd Length: 121  Bit Score: 144.26  E-value: 5.80e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1289857924   4 TLFKDFTFEAAHHLPHVPegHKCGRLHGHSFMVRLEITGEVDPHTGWIMDFAELKAAFKPTYDRLDHYYLNDIPGLE--N 81
Cdd:pfam01242   1 EITKEFRFDAAHRLPDYP--GKCSNLHGHNYRVEVTVRGEELDETGMVVDFGELKKAVKEVLDRLDHRFLNDDPEFEtlN 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1289857924  82 PTSEVLAKWIWDEMKPRV----PLLSAVMVKETCTAGCIYRGE 120
Cdd:pfam01242  79 PTAENLARYIFERLKPRLsgggVRLARVRVWETPTSWAEYRGE 121
 
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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