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Conserved domains on  [gi|472302335|gb|AGI37805|]
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alkane monooxygenase, partial [Rhizobium sp. X-b17]

Protein Classification

alkane 1-monooxygenase( domain architecture ID 10131413)

alkane 1-monooxygenase catalyzes the hydroxylation of n-alkanes and fatty acids in the presence of a NADH-rubredoxin reductase and rubredoxin

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Alkane-hydroxylase cd03512
Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement ...
 1-153 6.45e-78

Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes in Pseudomonas oleovorans encode conversion of alkanes to acyl CoA. The alkane omega-hydroxylase (AlkB) system is responsible for the initial oxidation of inactivated alkanes. It is a three-component system comprising a soluble NADH-rubredoxin reductase (AlkT), a soluble rubredoxin (AlkG), and the integral membrane oxygenase (AlkB). AlkB utilizes the oxygen rebound mechanism to hydroxylate alkanes. This mechanism involves homolytic cleavage of the C-H bond by an electrophilic metal-oxo intermediate to generate a substrate-based radical. As with other members of this superfamily, this domain family has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. The active site structure of AlkB is not known, however, spectroscopic and genetic evidence points to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals. Like all other members of this superfamily, there are eight conserved histidines seen in the histidine cluster motifs: HXXXH, HXXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the homolog, stearoyl CoA desaturase. Also included in this CD are terminal alkane hydroxylases (AlkM), xylene monooxygenase hydroxylases (XylM), p-cymene monooxygenase hydroxylases (CymAa), and other related proteins.


:

Pssm-ID: 239589  Cd Length: 314  Bit Score: 233.71  E-value: 6.45e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472302335   1 LGHKKEAFDRWMAKLVLAVVGYGHFFIEHNKGHHRDVATPKDPATSRMGENIYSFATREIPGAFKRAWELEEVRLERSGK 80
Cdd:cd03512   94 LIHRRSRLERWLGKLLLASLLYGHFAIEHVRGHHRYVATPEDPATARRGESFYRFLPRALVGSFRSAWKLEKKRLRRKGR 173

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 472302335  81 SVWSLDNEILQPLIITVVLYSGLLAFFGPIMLVFLPIQMAYGWWQLTSANYIEHYGLLREKLPNGKYEHQKPH 153
Cdd:cd03512  174 SPWSPRNEVLRYLALAVALLALAAALGGLAGLLFLLIQAFYAKSLLELVNYIEHYGLLRKKLANGRYEPVGPR 246
 
Name Accession Description Interval E-value
Alkane-hydroxylase cd03512
Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement ...
 1-153 6.45e-78

Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes in Pseudomonas oleovorans encode conversion of alkanes to acyl CoA. The alkane omega-hydroxylase (AlkB) system is responsible for the initial oxidation of inactivated alkanes. It is a three-component system comprising a soluble NADH-rubredoxin reductase (AlkT), a soluble rubredoxin (AlkG), and the integral membrane oxygenase (AlkB). AlkB utilizes the oxygen rebound mechanism to hydroxylate alkanes. This mechanism involves homolytic cleavage of the C-H bond by an electrophilic metal-oxo intermediate to generate a substrate-based radical. As with other members of this superfamily, this domain family has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. The active site structure of AlkB is not known, however, spectroscopic and genetic evidence points to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals. Like all other members of this superfamily, there are eight conserved histidines seen in the histidine cluster motifs: HXXXH, HXXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the homolog, stearoyl CoA desaturase. Also included in this CD are terminal alkane hydroxylases (AlkM), xylene monooxygenase hydroxylases (XylM), p-cymene monooxygenase hydroxylases (CymAa), and other related proteins.


Pssm-ID: 239589  Cd Length: 314  Bit Score: 233.71  E-value: 6.45e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472302335   1 LGHKKEAFDRWMAKLVLAVVGYGHFFIEHNKGHHRDVATPKDPATSRMGENIYSFATREIPGAFKRAWELEEVRLERSGK 80
Cdd:cd03512   94 LIHRRSRLERWLGKLLLASLLYGHFAIEHVRGHHRYVATPEDPATARRGESFYRFLPRALVGSFRSAWKLEKKRLRRKGR 173

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 472302335  81 SVWSLDNEILQPLIITVVLYSGLLAFFGPIMLVFLPIQMAYGWWQLTSANYIEHYGLLREKLPNGKYEHQKPH 153
Cdd:cd03512  174 SPWSPRNEVLRYLALAVALLALAAALGGLAGLLFLLIQAFYAKSLLELVNYIEHYGLLRKKLANGRYEPVGPR 246
FA_desaturase pfam00487
Fatty acid desaturase; Fatty acid desaturases are enzymes that catalyze the insertion of a ...
 3-137 1.75e-04

Fatty acid desaturase; Fatty acid desaturases are enzymes that catalyze the insertion of a double bond at the delta position of fatty acids. There seem to be two distinct families of fatty acid desaturases which do not seem to be evolutionary related: Family 1 composed of Stearoyl-CoA desaturases (SCD) and Family 2 composed of Bacterial fatty acid desaturases, Plant stearoyl-acyl-carrier-protein desaturase and Cyanobacterial DesA. Members of this entry are ER integral membrane proteins that share the same mushroom-shaped fold consisting of four transmembrane helices (TM1-TM4) which anchor them to the membrane, capped by a cytosolic domain containing a unique 9-10 histidine- coordinating di metal (di-iron) catalytic centre. The structure of mouse stearoyl-CoA desaturase (SDC) revealed that TM2 and TM4 are longer than TM1 and TM3 and protrude into the cytosolic domain, providing three of the nine histidine residues that coordinate the two metal ions, while the other histidine residues are provided by the soluble domain in this enzyme.


Pssm-ID: 425713 [Multi-domain]  Cd Length: 252  Bit Score: 40.02  E-value: 1.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472302335    3 HKKEAFDRWMAKLVLAVVG------YGHFFIEHNKGHHRDVATPKDPAT---SRMGENIYSFATREIPGAFKRAWELEEV 73
Cdd:pfam00487  32 FKKRRLNRWLNDLLGRLAGlplgisYSAWRIAHLVHHRYTNGPDKDPDTaplASRFRGLLRYLLRWLLGLLVLAWLLALV 111

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 472302335   74 RLE-RSGKSVWSLDNEILQP----------LIITVVLYSGLLAFFGPIMLVFLPIQMAYGWWQLTSANYIEHYGL 137
Cdd:pfam00487 112 LPLwLRRLARRKRPIKSRRRrwrliawlllLAAWLGLWLGFLGLGGLLLLLWLLPLLVFGFLLALIFNYLEHYGG 186
 
Name Accession Description Interval E-value
Alkane-hydroxylase cd03512
Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement ...
 1-153 6.45e-78

Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes in Pseudomonas oleovorans encode conversion of alkanes to acyl CoA. The alkane omega-hydroxylase (AlkB) system is responsible for the initial oxidation of inactivated alkanes. It is a three-component system comprising a soluble NADH-rubredoxin reductase (AlkT), a soluble rubredoxin (AlkG), and the integral membrane oxygenase (AlkB). AlkB utilizes the oxygen rebound mechanism to hydroxylate alkanes. This mechanism involves homolytic cleavage of the C-H bond by an electrophilic metal-oxo intermediate to generate a substrate-based radical. As with other members of this superfamily, this domain family has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. The active site structure of AlkB is not known, however, spectroscopic and genetic evidence points to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals. Like all other members of this superfamily, there are eight conserved histidines seen in the histidine cluster motifs: HXXXH, HXXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the homolog, stearoyl CoA desaturase. Also included in this CD are terminal alkane hydroxylases (AlkM), xylene monooxygenase hydroxylases (XylM), p-cymene monooxygenase hydroxylases (CymAa), and other related proteins.


Pssm-ID: 239589  Cd Length: 314  Bit Score: 233.71  E-value: 6.45e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472302335   1 LGHKKEAFDRWMAKLVLAVVGYGHFFIEHNKGHHRDVATPKDPATSRMGENIYSFATREIPGAFKRAWELEEVRLERSGK 80
Cdd:cd03512   94 LIHRRSRLERWLGKLLLASLLYGHFAIEHVRGHHRYVATPEDPATARRGESFYRFLPRALVGSFRSAWKLEKKRLRRKGR 173

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 472302335  81 SVWSLDNEILQPLIITVVLYSGLLAFFGPIMLVFLPIQMAYGWWQLTSANYIEHYGLLREKLPNGKYEHQKPH 153
Cdd:cd03512  174 SPWSPRNEVLRYLALAVALLALAAALGGLAGLLFLLIQAFYAKSLLELVNYIEHYGLLRKKLANGRYEPVGPR 246
FA_desaturase pfam00487
Fatty acid desaturase; Fatty acid desaturases are enzymes that catalyze the insertion of a ...
 3-137 1.75e-04

Fatty acid desaturase; Fatty acid desaturases are enzymes that catalyze the insertion of a double bond at the delta position of fatty acids. There seem to be two distinct families of fatty acid desaturases which do not seem to be evolutionary related: Family 1 composed of Stearoyl-CoA desaturases (SCD) and Family 2 composed of Bacterial fatty acid desaturases, Plant stearoyl-acyl-carrier-protein desaturase and Cyanobacterial DesA. Members of this entry are ER integral membrane proteins that share the same mushroom-shaped fold consisting of four transmembrane helices (TM1-TM4) which anchor them to the membrane, capped by a cytosolic domain containing a unique 9-10 histidine- coordinating di metal (di-iron) catalytic centre. The structure of mouse stearoyl-CoA desaturase (SDC) revealed that TM2 and TM4 are longer than TM1 and TM3 and protrude into the cytosolic domain, providing three of the nine histidine residues that coordinate the two metal ions, while the other histidine residues are provided by the soluble domain in this enzyme.


Pssm-ID: 425713 [Multi-domain]  Cd Length: 252  Bit Score: 40.02  E-value: 1.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 472302335    3 HKKEAFDRWMAKLVLAVVG------YGHFFIEHNKGHHRDVATPKDPAT---SRMGENIYSFATREIPGAFKRAWELEEV 73
Cdd:pfam00487  32 FKKRRLNRWLNDLLGRLAGlplgisYSAWRIAHLVHHRYTNGPDKDPDTaplASRFRGLLRYLLRWLLGLLVLAWLLALV 111

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 472302335   74 RLE-RSGKSVWSLDNEILQP----------LIITVVLYSGLLAFFGPIMLVFLPIQMAYGWWQLTSANYIEHYGL 137
Cdd:pfam00487 112 LPLwLRRLARRKRPIKSRRRrwrliawlllLAAWLGLWLGFLGLGGLLLLLWLLPLLVFGFLLALIFNYLEHYGG 186
 
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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