Conserved Protein Domain Family
PA_degradation_oxidoreductase_like

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cd06214: PA_degradation_oxidoreductase_like 
NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like domain with an iron-sulfur binding cluster domain. Ferredoxins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal portion may contain a flavin prosthetic group, as in flavoenzymes, or use flavin as a substrate. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria and participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH.
Statistics
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PSSM-Id: 99810
View PSSM: cd06214
Aligned: 81 rows
Threshold Bit Score: 214.715
Threshold Setting Gi: 160352243
Created: 27-Sep-2006
Updated: 2-Oct-2020
Structure
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Aligned Rows:
  next features
Feature 1:FAD binding pocket [chemical binding site]
Evidence:
  • Comment:contacts primarily in the N-terminal region
  • Comment:based on Acinetobacter sp. Benzoate dioxygenase reductase (1KRH) and Methylococcus capsulatus Methane monooxygenase (1TVC)

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                             #                            ####         
P76081        4 FHSLTVAKVESETRDav-tiTFAVPQPLqeayRFRPGQHLTLKas---------------fdGEELRRCYSICRSYLPg- 66  Escherichia coli
YP_678175     4 NNQVLIEEKINETADa---vTLVLKQHDsi-kNYKSGQFITLLln---------------igGEKVRRSYSFSSSPETds 64  Cytophaga hutchi...
AAK01349      3 TYSLRVERKQRETDDca-slWLSVPTDLrsafAHRPGQFIAVSae---------------inGEEVTRQYSLSSAPDDsr 66  Hyphomicrobium c...
AAW22511      3 TYHLKIISKRDEGNDta-slWLEVPQDLrgafSYQPGQFLTVEre---------------qsGERISRQYSLSSTPGAhr 66  Aminobacter sp. ...
CAH18517     33 TYPLKIAEKKTEAEDav-slYFDVPQDLkgafGYRPGQFLTIEte---------------dnGDAIARQYSLSSTPGSha 96  Rhodobacteraceae...
ZP_01693201   5 NYQLKVKEVVNETKDav-tvVFENPAEGa--lTYKPGQFLTLIfs---------------leGESVRRAYSLCSAPSIda 66  Microscilla mari...
ZP_01719098  17 YLPLKVREVVKETADtv-siYFEQPDPYl---DYKPGQFLTLVmd---------------feGKEQRRSYSLCTSPYVdp 77  Algoriphagus sp....
ZP_01886411   9 LFELRIAGMTFCPGEnl-liTFEPLDGAr--pSYKAGQFLTLVfr---------------vnGKELRRSYSLYSSPDAee 70  Pedobacter sp. B...
EDP78939     45 DLEVMVADVIEETADtttlvLFTGNDRL----DYLAGHFLTIDprqfpalerwvayledlkgKREAPRAYSLASAPHEr- 119 Anaeromyxobacter...
ZP_01463904  14 EYEPTVASVRMETPDt---aTLFLDFGGvp-lDYKAGQFLNIDphqfrelaplaaflqeqkgRREMFRSYSLSSAPHEp- 88  Stigmatella aura...
Feature 1           ### #            ###                                         #  #           
P76081       67 eISVAVKAIEG---------GRFSRYAREHIRqGMTLEVMVPQGHFGYQpqa-erqGRYLAIAAGSGITPMLAIIATTLQ 136 Escherichia coli
YP_678175    65 kPSITIKKIQD---------GKASTYLFNTIKaGDSLEFQQPAGIFTLDka---ssESLVFIGAGSGITPLISMIKTALA 132 Cytophaga hutchi...
AAK01349     67 gIRITVKKIPG---------GRMSSWLVDRVNeGDRIEVAAPRGRFFRPld---raHRVLLLAAGSGIAPILPIAQKLLA 134 Hyphomicrobium c...
AAW22511     67 dLRITVKKIPG---------GAVSPWLVDIAGqGQALEVQVPRGRFFRGfn---esRHVLMLACGSGIAPVLSIARHLLA 134 Aminobacter sp. ...
CAH18517     97 qLRITIKKIEG---------GRVSTWLVDEAAeGDLIEVQIPRGRFFKEld---apSHVVLLAAGSGIAPILSIGRWLLE 164 Rhodobacteraceae...
ZP_01693201  67 qPAVTVKRVEG---------GKVSNHINDHVKaGDTIEVMAPAGVFTADvnk-knkRHVVLFAGGSGITPMMSIMQTVLN 136 Microscilla mari...
ZP_01719098  78 fPGISVKRVPG---------GLFSNFLNEKIHpGKTLNVLKPLGNFTTDfhs-knqKHFFLIGGGSGITPLMGILKSVIA 147 Algoriphagus sp....
ZP_01886411  71 pMSIGIKRVEN---------GAISRLLHHKTAiGEILTAVEPNGLFNYVpey-slkRTVFLFGAGIGITPLFSILKTALI 140 Pedobacter sp. B...
EDP78939    120 yLAITVKEETYqsgr-trypPLLSPMLVRRTPrGSRFVITGFTGPYVLPprveektDHLVHVVAGSGSVPNWSILKHALR 198 Anaeromyxobacter...
ZP_01463904  89 lVAITVKDEVFlpgltrypaLLAPLLVHGRLA-GARLKVSGFMGPYVLPddvesrtDHIVHVVAGSGAVPNFSIIKDALH 167 Stigmatella aura...
Feature 1                                                                                       
P76081      137 tepesQFTLIYGNRTsqsMMFRQALADLKDKYpqRLQLLCIFSQETLDsdl----lhGRIDGEKLqslgasli--nfrly 210 Escherichia coli
YP_678175   133 nkkfkKICLIYSNRNedsVIFKKKLEELKAAYs-NFEVIYTYSQPHDTsl-----pkGRLNQSQFikiiehikd-lavak 205 Cytophaga hutchi...
AAK01349    135 dgvghRITLAYGSRAlddIILRKDVDELPNIFr-TCALEHVLSRPGPTwdg----prGRLDSAYLlsrqdlwdgnashlp 209 Hyphomicrobium c...
AAW22511    135 ldaghRVTIVYGNRTpdaIILRDEVRELAESYpdVCRVEHVMSRAGEGwqg----arGRIDRAFIlsrmedwlaagqglp 210 Aminobacter sp. ...
CAH18517    165 ndeghKITLVYGNRTpdtVILADEVNEIETQFadRCMVQHVMSRANGNwdg----drGRIDRKYVtrqfpdwddrsgdlp 240 Rhodobacteraceae...
ZP_01693201 137 tessaVVSLVYANRDeesIIFKDKIDGLKAKYgkQLNIVHVLENPPAGwsg----ysGRLTPDLVqailkslpk-klfkp 211 Microscilla mari...
ZP_01719098 148 nepksKVTLLYCSRHeehIIFKKELDALEEKYe-QLTVIHNLSQPTEAwtg----lkGRLTRETIsdfvkkaea-egefq 221 Algoriphagus sp....
ZP_01886411 141 rerdsRVVLVYSSRSveeTLFYEELRLLQVEHpdRLKVINVISQSQNLl-------mARLNGPLIerivktelm-ydkee 212 Pedobacter sp. B...
EDP78939    199 ehprlRHTFVYSNRTwddVIYRDGLRQLAAEHpdRLRVVHTLTREPEPerrgpgvrrGRISAELLrelvpd------pra 272 Anaeromyxobacter...
ZP_01463904 168 rglklRHTFLLSNKTaadMLYRDALEALEAAHpdQLRVVHTLTRETETshlgprvrrGRVDQALLeelipd------ret 241 Stigmatella aura...
Feature 1                                                        # # 
P76081      211 deaFICGPAA------------------MMDDAETALKALGMPDKTIHLERFN 245 Escherichia coli
YP_678175   206 tdyFLCGPDG------------------MLEEVKHGLEILQVASSKIHKESFV 240 Cytophaga hutchinsonii ATCC 33406
AAK01349    210 livYLCGPES------------------FMDAAEAFFLSHGVDASAIRRESFD 244 Hyphomicrobium chloromethanicum
AAW22511    211 psiFLCGPQE------------------FMDAAEATFTEKGVALKDIHRESFD 245 Aminobacter sp. CC495
CAH18517    241 mifYMCGPEG------------------FMDAAESALQQFGVPLKSIHRESFD 275 Rhodobacteraceae bacterium 198
ZP_01693201 212 reyFMCGPAG------------------MMEQIEVTFQKYKLPKDKLRKESFT 246 Microscilla marina ATCC 23134
ZP_01719098 222 teyFICGPEG------------------ILETSIEVLDSLTIDSSKVHKESFY 256 Algoriphagus sp. PR1
ZP_01886411 213 allYTCGPVD------------------YMDVCRITLLNLGFDKSQIRRETFV 247 Pedobacter sp. BAL39
EDP78939    273 alwYACGPAVgpieraaakergetpaprFLEAALAALDELGVPRDRVKRESYG 325 Anaeromyxobacter sp. K
ZP_01463904 242 clvYTCGPAItpwdrrkaletrtpasprFLETVVGHLHTLGIHDKRIKREAYG 294 Stigmatella aurantiaca DW4/3-1

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