2B1X,2B24,1EG9,1ULJ,3EN1,2GBW,2CKF,2BMO,1WQL,3GZX


Conserved Protein Domain Family
RHO_alpha_C_NDO-like

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cd08881: RHO_alpha_C_NDO-like 
Click on image for an interactive view with Cn3D
C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases
C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). This domain binds non-heme Fe(II). RHOs utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents form the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and a C-terminal domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. Proteins belonging to this subgroup include the terminal oxygenase alpha subunits of biphenyl dioxygenase, cumene dioxygenase from Pseudomonas fluorescens IP01, ethylbenzene dioxygenase, naphthalene 1,2-dioxygenase, nitrobenzene dioxygenase from Comamonas sp. strain JS765, toluene 2,3-dioxygenase from Pseudomonas putida F1, dioxin dioxygenase of Sphingomonas sp. Strain RW1, and the polycyclic aromatic hydrocarbons (PAHs)degrading ring-hydroxylating dioxygenase from Sphingomonas CHY-1. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket.
Statistics
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PSSM-Id: 176890
View PSSM: cd08881
Aligned: 49 rows
Threshold Bit Score: 204.018
Threshold Setting Gi: 119714930
Created: 30-Jul-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:based on substrate and Fe(II) binding sites of various RHO_alpha_C_NDO-like domains
  • Structure:1EG9_A; Pseudomonas putida oxygenase component of naphthalene 1,2-dioxygenase binds indole (contacts at 4A) and Fe (II).
    View structure with Cn3D
  • Structure:3EN1_A; Pseudomonas putida oxygenase component of toluene 2,3-dioxygenase binds toluene (contacts at 4A) and Fe(II).
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                              ##  ## ##   #                                             
2B1X_A       187 GLQVVGAPQRWVIDANWKLGADNFVgDAYHTmMTHRSMVelglapp---------dpqfalyGEHIHTg---------hG 248 Rhodococcus sp....
1EG9_A       179 GLELVGPPGKVVIKANWKAPAENFVgDAYHVgWTHASSLrsgesifssla--gnaalppegaGLQMTSk---------yG 247 Pseudomonas putida
BAB62289     174 SGLEVRGPQRWRVKANWKIGAENFAgDMYHTpQTHTSVVeiglfrep--------kaekrkdGATYWA-----------G 234 Rhodococcus sp....
YP_002523623 183 GTEVYAPPERWVADTDWKICAENFGgDGYHTpVAHQFGFalgfyps---------tgrthfmGFAAHIpg--------rG 245 Thermomicrobium...
YP_555834    190 GLEVLGPPQRFVVRANWKAAGEQSAaDGYHTlTLHRWLGevgnyshvkdkdsgandltqqmyGVEISSp---------hG 260 Burkholderia xe...
YP_256646    177 GMKIVGKPIKFIADFDWKSGASNFAeDRLHTiTTHRSVVelgyaspi-------srfgyvtpGLSEITacyl---ndslG 246 Sulfolobus acid...
YP_001072458 196 GMTVLGHPQRFIIKANWKSAAEQFAgDIFHTlSLHRSMQelqllsteg------etqepamaGVSASYn----------G 259 Mycobacterium s...
EAZ58742     190 GMEVLGPPQRFIVNANWKTAGEQSAaDGFHTlTLHRWLGevgnyakkgegegegadlspemiGVEVSSp---------hG 260 Pseudomonas aer...
YP_001683544 190 GLEVLGPPQRFTIKANWKTACEQSAaDGFHTlTLHRWLGefakfgdg--------dlttsmyGTEVGSl---------qG 252 Caulobacter sp....
YP_001683600 191 GMEVLGPPQRFIIRANWKTACEQSAsDGFHTlTLHRWLGevgpyak---------kpeaegqGADLAAemggcevwtdgG 261 Caulobacter sp....
Feature 1                                                                       # #         #    
2B1X_A       249 HGLGIIGPppgmplpefmglpenive-------------------elerrltpeqveifrptAFIHGTVFPNLSIGNflm 309 Rhodococcus sp....
1EG9_A       248 SGMGVLWDgysgvhsadlvpelmafgg----------------akqerlnkeigdvrariyrSHLNCTVFPNNSMLTc-- 309 Pseudomonas putida
BAB62289     235 PGGGTTYKlpdgtfdermqyvgytaemt--------------drakevwsdeqqrvigadgfMISAASVFPNLSFVHnwp 300 Rhodococcus sp....
YP_002523623 246 HCIGIGHTpglppfpgfppevveg----------------------yqqaltpeqisvfrdaRMAVATVFPNLSFLIqpf 303 Thermomicrobium...
YP_555834    261 HALRCQDLarkirrltgkepadltpeerfrvlpp--pgmtadmvpqllrhlgkeqidvmasmPPQVGGIFPNVLFAFlyl 338 Burkholderia xe...
YP_256646    247 RPVGAFGMrfppeesipgffgfygdhfr---------------ehskpegvseeqykvfqrvSHWVGTIFPNLSFFTaad 311 Sulfolobus acid...
YP_001072458 260 HFVRCFDLtqehyvnalkgknlaemtpmerlhlvpppgmspdmvdglaerfddgqlkilaefTPQVGQLWPNVAALCmpf 339 Mycobacterium s...
EAZ58742     261 HALRCIDLarkikrltgldpetlsvqekldalpp--agmtadmveqlarnlsedqlkvltsmPPQVGGMFPNILFGFvyi 338 Pseudomonas aer...
YP_001683544 253 HALRCMPVankfkqaagfrdgnltleeklaivpp--pgitkemlpelirnltpeqlgllvdsPPQVGGMFPNVLIAFiyv 330 Caulobacter sp....
YP_001683600 262 HTMRCIDLdrkirritgrdpselsaaeklallpp--pgmtpemvpellerfdddhlrlmawrPPQVGNFFPNGLFEFiyl 339 Caulobacter sp....
Feature 1                                                             #     #   #                
2B1X_A       310 gkdh-lsaptafLTLRLWHPLGPDKMEVMSFFLVEKDAPDWFKDESYKSYLRTFGISGGFEQDDAENWRSITRVMGGQFA 388 Rhodococcus sp....
1EG9_A       310 -----------sGVFKVWNPIDANTTEVWTYAIVEKDMPEDLKRRLADSVQRTFGPAGFWESDDNDNMETASQNGKKYQS 378 Pseudomonas putida
BAB62289     301 kved-gddvlpfISIRLWQPISENETEVLSFFAVDRSAPEEFKKKSYKAYLMCFGSTGMFEQDDVENWVSLTNTSAGSMA 379 Rhodococcus sp....
YP_002523623 304 sltp-gkpglkfCTMRLWHPRGPGRIEMWTWCLVPKHISPELKREIYRVYSLAFGAAGTFEQDDFENWTNLSRQNAAFNA 382 Thermomicrobium...
YP_555834    339 pqpd--gsslgaIALHTYVPRGPDKLEFTNWVFVEKDTPADVREKMRKQSTQLLGTTGMVEQDDSDTWPHMTLAAKGAMG 416 Burkholderia xe...
YP_256646    312 qtdksgkpnspvSLIRLWQPIGPGKTEVWTWVVVPRVLPDEIAKRVYEVTTSHFGPSGVAEMDDTAIWRRISKSASGNLA 391 Sulfolobus acid...
YP_001072458 340 qfpd--gtpsafLSWRVWVPRGPEHFELFHWSLVERDAPQELRDTVNLMTAATFGISGFVEADDTDTWPMQTHAARGALG 417 Mycobacterium s...
EAZ58742     339 pqpd--ggvvgsMTMHAYVPQGPDKLEFVNWIFAEKDAPAELREKMLKQTIQLFGTSGMVEQDDSDTWPHMTLAAKGAMG 416 Pseudomonas aer...
YP_001683544 331 pqpd--geiiglTSLHTYIPKGPDELEFCNFIMAEKDAPEEHKQRALQFAVRMLGTSGMVEQDDSDTWPHITQTAKGAAA 408 Caulobacter sp....
YP_001683600 340 pqpd--gtvagaMALHAYVPKGPDKLEFMNWIFAEKDTPPALKARMLRQSIQLLGTSGMVEQDDSDTWPHQTIVAKGAVS 417 Caulobacter sp....
Feature 1                                                                
2B1X_A       389 KTGELNYQMGRGVl--------ePDPnwtGPGEAYPlDYAEANQRNFLEYWMQLML 436 Rhodococcus sp. NCIMB12038
1EG9_A       379 RDSDLLSNLGFGEdv-------yGDAv--YPGVVGKsAIGETSYRGFYRAYQAHVS 425 Pseudomonas putida
BAB62289     380 RRLLLNSRMGLLEdgtrvsdeltADEf-hGPGTAQV-GYNEANQRKLLEMWADYLE 433 Rhodococcus sp. RHA1
YP_002523623 383 DTFELAYLQGLDWep------lsDFP---GPGYAFTpYVTEIGFRNLWGTWLNYLL 429 Thermomicrobium roseum DSM 5159
YP_555834    417 RKMTLKYQAAYETga------peGWP---GPGIVNEgFTKDDTQWHWWQYWLELMT 463 Burkholderia xenovorans LB400
YP_256646    392 RRISQLIIGGLDSvsdl---pvlRDWr--GPGLVRPtQFHEDGPRTFWKRWLMEMG 442 Sulfolobus acidocaldarius DSM 639
YP_001072458 418 KDQKLRYQAITGEhk------pdDWP---GPGEIYAgFPKDDTQWNFWVRYTEMME 464 Mycobacterium sp. JLS
EAZ58742     417 RQMTLKYQACYETga------peGWP---GPGIVNEgFTKDDTQWHWWQYWHELMT 463 Pseudomonas aeruginosa 2192
YP_001683544 409 RNVTMKYQAVCTTpp------rpDWP---GPALVYEgFTKDDTQWNWWLAYRDLMN 455 Caulobacter sp. K31
YP_001683600 418 KDITMKYQALYETgr------paNWP---GPGHVGEgFTKDDTQWQWWKSWYDLMV 464 Caulobacter sp. K31

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