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Conserved domains on  [gi|489501159|ref|WP_003406060|]
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MULTISPECIES: PPOX class F420-dependent oxidoreductase [Mycobacterium]

Protein Classification

PPOX class F420-dependent oxidoreductase( domain architecture ID 11497257)

PPOX class F420-dependent oxidoreductase similar to Mycobacterium tuberculosis F420H(2)-dependent biliverdin reductase, which catalyzes the reduction of biliverdin-IXalpha at the C10 position to form bilirubin-IXalpha, a potent antioxidant

CATH:  2.30.110.10
EC:  1.-.-.-
Gene Ontology:  GO:0016491|GO:0070967
PubMed:  15620716
SCOP:  4002129

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 10-141 3.53e-42

PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomyces, make F420. The Partial Phylogenetic Profiling algorithm identifies this members of this protein family as high-scoring proteins to the F420 biosynthesis profile. A member of this family, Rv1155, was crytallized after expression in Escherichia coli, which does not synthesize F420; the crystal structure shown to resemble FMN-binding proteins, but with a recognizable empty cleft corresponding to, yet differing profounding from, the FMN site of pyridoxine 5'-phosphate oxidase. We propose that this protein family consists of F420-binding enzymes. [Unknown function, Enzymes of unknown specificity]


:

Pssm-ID: 274679 [Multi-domain]  Cd Length: 126  Bit Score: 136.27  E-value: 3.53e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489501159   10 LLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLiqVSIAEPRAKTRNLRRDPRASILVDADDGW-SYAVAEGTAQL 88
Cdd:TIGR03618   1 LRDLLSERRLAVLATIRPDGRPQLSPVWFALDGDELV--FSTTAGRAKARNLRRDPRVSLSVLDPDGPyRYVEIEGTAEV 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 489501159   89 TpPAAAPDDDTVEALIALYRNIAGEhpdwDDYRQAMVTDRRVLLTLPISHVYG 141
Cdd:TIGR03618  79 S-PDPDAVRDLVDRLAERYRGAAGE----DEYRRPMVDPRRVVVRVTPERVYG 126
 
Name Accession Description Interval E-value
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 10-141 3.53e-42

PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomyces, make F420. The Partial Phylogenetic Profiling algorithm identifies this members of this protein family as high-scoring proteins to the F420 biosynthesis profile. A member of this family, Rv1155, was crytallized after expression in Escherichia coli, which does not synthesize F420; the crystal structure shown to resemble FMN-binding proteins, but with a recognizable empty cleft corresponding to, yet differing profounding from, the FMN site of pyridoxine 5'-phosphate oxidase. We propose that this protein family consists of F420-binding enzymes. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 274679 [Multi-domain]  Cd Length: 126  Bit Score: 136.27  E-value: 3.53e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489501159   10 LLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLiqVSIAEPRAKTRNLRRDPRASILVDADDGW-SYAVAEGTAQL 88
Cdd:TIGR03618   1 LRDLLSERRLAVLATIRPDGRPQLSPVWFALDGDELV--FSTTAGRAKARNLRRDPRVSLSVLDPDGPyRYVEIEGTAEV 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 489501159   89 TpPAAAPDDDTVEALIALYRNIAGEhpdwDDYRQAMVTDRRVLLTLPISHVYG 141
Cdd:TIGR03618  79 S-PDPDAVRDLVDRLAERYRGAAGE----DEYRRPMVDPRRVVVRVTPERVYG 126
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
3-141 6.33e-21

General stress protein 26 (function unknown) [Function unknown];


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 82.29  E-value: 6.33e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489501159   3 RQVFDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVA 82
Cdd:COG3871    4 DEELEEKLWELLEDIRTAMLATVDADGRPHSRPMWFQVDVDDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPGDDRYVSV 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489501159  83 EGTAQLTPPaAAPDDDTVEALIALYRNIAGEHPDwddyrqamvtdrRVLLTLPISHVYG 141
Cdd:COG3871   84 EGTAEIVDD-RAKIDELWNPLAEAWFPDGPDDPD------------LVLLRVTPERAEY 129
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 6-93 2.57e-17

Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family members were predicted to encode pyridoxamine 5'-phosphate oxidase, based on sequence similarity. However, there is no experimental data to validate the predicted activity and purified proteins, such as Swiss:Q06199 and its paralogs, do not possess this activity, nor do they bind to flavin mononucleotide (FMN). To date, the only time functional oxidase activity has been experimentally demonstrated is when the sequences contain both pfam01243 and pfam10590. Moreover, some of the family members that contain both domains have been shown to be involved in phenazine biosynthesis. While some molecular function has been experimentally validated for the proteins containing both domains, the role performed by each domain on its own is unknown.


Pssm-ID: 426149 [Multi-domain]  Cd Length: 88  Bit Score: 71.51  E-value: 2.57e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489501159    6 FDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGT 85
Cdd:pfam01243   1 LTEEIREFLAEPNAVVLATVDKDGRPNVRPVGLKYGFDTVGILFATNTDSRKARNLEENPRVALLFGDPELRRGVRIEGT 80


                  ....*...
gi 489501159   86 AQLTPPAA 93
Cdd:pfam01243  81 AEIVTDGE 88
 
Name Accession Description Interval E-value
Rv1155_F420 TIGR03618
PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for ...
 10-141 3.53e-42

PPOX class probable F420-dependent enzyme; A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomyces, make F420. The Partial Phylogenetic Profiling algorithm identifies this members of this protein family as high-scoring proteins to the F420 biosynthesis profile. A member of this family, Rv1155, was crytallized after expression in Escherichia coli, which does not synthesize F420; the crystal structure shown to resemble FMN-binding proteins, but with a recognizable empty cleft corresponding to, yet differing profounding from, the FMN site of pyridoxine 5'-phosphate oxidase. We propose that this protein family consists of F420-binding enzymes. [Unknown function, Enzymes of unknown specificity]


Pssm-ID: 274679 [Multi-domain]  Cd Length: 126  Bit Score: 136.27  E-value: 3.53e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489501159   10 LLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLiqVSIAEPRAKTRNLRRDPRASILVDADDGW-SYAVAEGTAQL 88
Cdd:TIGR03618   1 LRDLLSERRLAVLATIRPDGRPQLSPVWFALDGDELV--FSTTAGRAKARNLRRDPRVSLSVLDPDGPyRYVEIEGTAEV 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 489501159   89 TpPAAAPDDDTVEALIALYRNIAGEhpdwDDYRQAMVTDRRVLLTLPISHVYG 141
Cdd:TIGR03618  79 S-PDPDAVRDLVDRLAERYRGAAGE----DEYRRPMVDPRRVVVRVTPERVYG 126
YzzA COG3871
General stress protein 26 (function unknown) [Function unknown];
3-141 6.33e-21

General stress protein 26 (function unknown) [Function unknown];


Pssm-ID: 443080 [Multi-domain]  Cd Length: 132  Bit Score: 82.29  E-value: 6.33e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489501159   3 RQVFDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVA 82
Cdd:COG3871    4 DEELEEKLWELLEDIRTAMLATVDADGRPHSRPMWFQVDVDDGTLWFFTSRDSAKVRNIRRDPRVSLSFADPGDDRYVSV 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489501159  83 EGTAQLTPPaAAPDDDTVEALIALYRNIAGEHPDwddyrqamvtdrRVLLTLPISHVYG 141
Cdd:COG3871   84 EGTAEIVDD-RAKIDELWNPLAEAWFPDGPDDPD------------LVLLRVTPERAEY 129
Putative_PNPOx pfam01243
Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family ...
 6-93 2.57e-17

Pyridoxamine 5'-phosphate oxidase; Family of domains with putative PNPOx function. Family members were predicted to encode pyridoxamine 5'-phosphate oxidase, based on sequence similarity. However, there is no experimental data to validate the predicted activity and purified proteins, such as Swiss:Q06199 and its paralogs, do not possess this activity, nor do they bind to flavin mononucleotide (FMN). To date, the only time functional oxidase activity has been experimentally demonstrated is when the sequences contain both pfam01243 and pfam10590. Moreover, some of the family members that contain both domains have been shown to be involved in phenazine biosynthesis. While some molecular function has been experimentally validated for the proteins containing both domains, the role performed by each domain on its own is unknown.


Pssm-ID: 426149 [Multi-domain]  Cd Length: 88  Bit Score: 71.51  E-value: 2.57e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489501159    6 FDDKLLAVISGNSIGVLATIKHDGRPQLSNVQYHFDPRKLLIQVSIAEPRAKTRNLRRDPRASILVDADDGWSYAVAEGT 85
Cdd:pfam01243   1 LTEEIREFLAEPNAVVLATVDKDGRPNVRPVGLKYGFDTVGILFATNTDSRKARNLEENPRVALLFGDPELRRGVRIEGT 80


                  ....*...
gi 489501159   86 AQLTPPAA 93
Cdd:pfam01243  81 AEIVTDGE 88
HugZ COG0748
Putative heme iron utilization protein, contains PNPOx domain [Inorganic ion transport and ...
 20-122 1.72e-06

Putative heme iron utilization protein, contains PNPOx domain [Inorganic ion transport and metabolism];


Pssm-ID: 440511 [Multi-domain]  Cd Length: 221  Bit Score: 45.72  E-value: 1.72e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489501159  20 GVLATIKHDGRPQLSNVQYHFDPRK-LLIQVS-IAEpraKTRNLRRDPRASILVDADDGWS---YAVA----EGTAQLtp 90
Cdd:COG0748   22 GALATLDADGYPFASYAPFALDDDGsPYILISgLAE---HTRNLLADPRASLLLIEDESKAgdpLARPrltlQGRAER-- 96

                         90       100       110
                 ....*....|....*....|....*....|..
gi 489501159  91 paaAPDDDTVEALIALYRNIageHPDWDDYRQ 122
Cdd:COG0748   97 ---VEDSEEWEAARARYLAR---FPKAALYAD 122
 
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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