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: 17-Jan-2013
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:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                              #                            ####         
gi 13632702    4 FHSLTVAKVESETRDav-tiTFAVPQPLqeayRFRPGQHLTLKas---------------fdGEELRRCYSICRSYLPg- 66
gi 110637968   4 NNQVLIEEKINETADa---vTLVLKQHDsi-kNYKSGQFITLLln---------------igGEKVRRSYSFSSSPETds 64
gi 37594606    3 TYSLRVERKQRETDDca-slWLSVPTDLrsafAHRPGQFIAVSae---------------inGEEVTRQYSLSSAPDDsr 66
gi 56684778    3 TYHLKIISKRDEGNDta-slWLEVPQDLrgafSYQPGQFLTVEre---------------qsGERISRQYSLSSTPGAhr 66
gi 67008227   33 TYPLKIAEKKTEAEDav-slYFDVPQDLkgafGYRPGQFLTIEte---------------dnGDAIARQYSLSSTPGSha 96
gi 124008508   5 NYQLKVKEVVNETKDav-tvVFENPAEGa--lTYKPGQFLTLIfs---------------leGESVRRAYSLCSAPSIda 66
gi 126646588  17 YLPLKVREVVKETADtv-siYFEQPDPYl---DYKPGQFLTLVmd---------------feGKEQRRSYSLCTSPYVdp 77
gi 149280289   9 LFELRIAGMTFCPGEnl-liTFEPLDGAr--pSYKAGQFLTLVfr---------------vnGKELRRSYSLYSSPDAee 70
gi 160352243  45 DLEVMVADVIEETADtttlvLFTGNDRL----DYLAGHFLTIDprqfpalerwvayledlkgKREAPRAYSLASAPHEr- 119
gi 115376676  14 EYEPTVASVRMETPDt---aTLFLDFGGvp-lDYKAGQFLNIDphqfrelaplaaflqeqkgRREMFRSYSLSSAPHEp- 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1            ### #            ###                                         #  #           
gi 13632702   67 eISVAVKAIEG---------GRFSRYAREHIRqGMTLEVMVPQGHFGYQpqa-erqGRYLAIAAGSGITPMLAIIATTLQ 136
gi 110637968  65 kPSITIKKIQD---------GKASTYLFNTIKaGDSLEFQQPAGIFTLDka---ssESLVFIGAGSGITPLISMIKTALA 132
gi 37594606   67 gIRITVKKIPG---------GRMSSWLVDRVNeGDRIEVAAPRGRFFRPld---raHRVLLLAAGSGIAPILPIAQKLLA 134
gi 56684778   67 dLRITVKKIPG---------GAVSPWLVDIAGqGQALEVQVPRGRFFRGfn---esRHVLMLACGSGIAPVLSIARHLLA 134
gi 67008227   97 qLRITIKKIEG---------GRVSTWLVDEAAeGDLIEVQIPRGRFFKEld---apSHVVLLAAGSGIAPILSIGRWLLE 164
gi 124008508  67 qPAVTVKRVEG---------GKVSNHINDHVKaGDTIEVMAPAGVFTADvnk-knkRHVVLFAGGSGITPMMSIMQTVLN 136
gi 126646588  78 fPGISVKRVPG---------GLFSNFLNEKIHpGKTLNVLKPLGNFTTDfhs-knqKHFFLIGGGSGITPLMGILKSVIA 147
gi 149280289  71 pMSIGIKRVEN---------GAISRLLHHKTAiGEILTAVEPNGLFNYVpey-slkRTVFLFGAGIGITPLFSILKTALI 140
gi 160352243 120 yLAITVKEETYqsgr-trypPLLSPMLVRRTPrGSRFVITGFTGPYVLPprveektDHLVHVVAGSGSVPNWSILKHALR 198
gi 115376676  89 lVAITVKDEVFlpgltrypaLLAPLLVHGRLA-GARLKVSGFMGPYVLPddvesrtDHIVHVVAGSGAVPNFSIIKDALH 167
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                        
gi 13632702  137 tepesQFTLIYGNRTsqsMMFRQALADLKDKYpqRLQLLCIFSQETLDsdl----lhGRIDGEKLqslgasli--nfrly 210
gi 110637968 133 nkkfkKICLIYSNRNedsVIFKKKLEELKAAYs-NFEVIYTYSQPHDTsl-----pkGRLNQSQFikiiehikd-lavak 205
gi 37594606  135 dgvghRITLAYGSRAlddIILRKDVDELPNIFr-TCALEHVLSRPGPTwdg----prGRLDSAYLlsrqdlwdgnashlp 209
gi 56684778  135 ldaghRVTIVYGNRTpdaIILRDEVRELAESYpdVCRVEHVMSRAGEGwqg----arGRIDRAFIlsrmedwlaagqglp 210
gi 67008227  165 ndeghKITLVYGNRTpdtVILADEVNEIETQFadRCMVQHVMSRANGNwdg----drGRIDRKYVtrqfpdwddrsgdlp 240
gi 124008508 137 tessaVVSLVYANRDeesIIFKDKIDGLKAKYgkQLNIVHVLENPPAGwsg----ysGRLTPDLVqailkslpk-klfkp 211
gi 126646588 148 nepksKVTLLYCSRHeehIIFKKELDALEEKYe-QLTVIHNLSQPTEAwtg----lkGRLTRETIsdfvkkaea-egefq 221
gi 149280289 141 rerdsRVVLVYSSRSveeTLFYEELRLLQVEHpdRLKVINVISQSQNLl-------mARLNGPLIerivktelm-ydkee 212
gi 160352243 199 ehprlRHTFVYSNRTwddVIYRDGLRQLAAEHpdRLRVVHTLTREPEPerrgpgvrrGRISAELLrelvpd------pra 272
gi 115376676 168 rglklRHTFLLSNKTaadMLYRDALEALEAAHpdQLRVVHTLTRETETshlgprvrrGRVDQALLeelipd------ret 241
                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|...
Feature 1                                                         # # 
gi 13632702  211 deaFICGPAA------------------MMDDAETALKALGMPDKTIHLERFN 245
gi 110637968 206 tdyFLCGPDG------------------MLEEVKHGLEILQVASSKIHKESFV 240
gi 37594606  210 livYLCGPES------------------FMDAAEAFFLSHGVDASAIRRESFD 244
gi 56684778  211 psiFLCGPQE------------------FMDAAEATFTEKGVALKDIHRESFD 245
gi 67008227  241 mifYMCGPEG------------------FMDAAESALQQFGVPLKSIHRESFD 275
gi 124008508 212 reyFMCGPAG------------------MMEQIEVTFQKYKLPKDKLRKESFT 246
gi 126646588 222 teyFICGPEG------------------ILETSIEVLDSLTIDSSKVHKESFY 256
gi 149280289 213 allYTCGPVD------------------YMDVCRITLLNLGFDKSQIRRETFV 247
gi 160352243 273 alwYACGPAVgpieraaakergetpaprFLEAALAALDELGVPRDRVKRESYG 325
gi 115376676 242 clvYTCGPAItpwdrrkaletrtpasprFLETVVGHLHTLGIHDKRIKREAYG 294

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