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(-) Description

Title :  CRYSTAL STRUCTURE OF NON-HEME IRON OXYGENASE ORFP D157A MUTANT IN COMPLEX WITH (3S)-HYDROXY-L-ARG
 
Authors :  C. Y. Chang, Y. C. Liu, S. Y. Lyu, C. C. Wu, T. L. Li
Date :  28 Oct 13  (Deposition) - 18 Jun 14  (Release) - 18 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Oxygenase, Hydroxylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Y. Chang, S. Y. Lyu, Y. C. Liu, N. S. Hsu, C. C. Wu, C. F. Tang, K. H. Lin, J. Y. Ho, C. J. Wu, M. D. Tsai, T. L. Li
Biosynthesis Of Streptolidine Involved Two Unexpected Intermediates Produced By A Dihydroxylase And A Cyclase Through Unusual Mechanisms
Angew. Chem. Int. Ed. Engl. V. 53 1943 2014
PubMed-ID: 24505011  |  Reference-DOI: 10.1002/ANIE.201307989

(-) Compounds

Molecule 1 - L-ARGININE BETA-HYDROXYLASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: STREPTOMYCES LAVENDULAE
    Organism Taxid: 58340
    Synonym: NON-HEME IRON OXYGENASE ORFP

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1FE4Ligand/IonFE (III) ION
2SIN2Ligand/IonSUCCINIC ACID
3ZZU2Ligand/Ion(2S,3S)-3-HYDROXYARGININE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2SIN-1Ligand/IonSUCCINIC ACID
3ZZU-1Ligand/Ion(2S,3S)-3-HYDROXYARGININE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2SIN2Ligand/IonSUCCINIC ACID
3ZZU2Ligand/Ion(2S,3S)-3-HYDROXYARGININE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:154 , GLU A:156 , HIS A:303BINDING SITE FOR RESIDUE FE A 401
2AC2SOFTWAREHIS B:154 , GLU B:156 , HIS B:303 , ARG B:321BINDING SITE FOR RESIDUE FE B 401
3AC3SOFTWAREHIS C:154 , GLU C:156 , HIS C:303 , ARG C:321 , SIN C:402 , ZZU C:403BINDING SITE FOR RESIDUE FE C 401
4AC4SOFTWAREILE C:132 , LEU C:151 , THR C:180 , ARG C:317 , ARG C:321 , FE C:401BINDING SITE FOR RESIDUE SIN C 402
5AC5SOFTWAREGLN C:123 , LEU C:143 , GLY C:144 , HIS C:154 , GLU C:156 , ASP C:208 , SER C:210 , ASP C:255 , PHE C:258 , ARG C:321 , FE C:401BINDING SITE FOR RESIDUE ZZU C 403
6AC6SOFTWAREHIS D:154 , GLU D:156 , HIS D:303 , ARG D:321 , SIN D:402 , ZZU D:403BINDING SITE FOR RESIDUE FE D 401
7AC7SOFTWARELEU D:151 , THR D:180 , HIS D:303 , ARG D:305 , ARG D:317 , ARG D:321 , FE D:401BINDING SITE FOR RESIDUE SIN D 402
8AC8SOFTWAREGLN D:123 , GLN D:142 , LEU D:143 , HIS D:154 , GLU D:156 , ASP D:208 , SER D:210 , ASP D:255 , PHE D:258 , ARG D:321 , FE D:401 , HOH D:576BINDING SITE FOR RESIDUE ZZU D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NE0)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Arg A:96 -Pro A:97
2Arg B:96 -Pro B:97
3Arg C:96 -Pro C:97
4Thr C:229 -Ile C:230
5Arg D:96 -Pro D:97

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NE0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NE0)

(-) Exons   (0, 0)

(no "Exon" information available for 4NE0)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeee....hhhhhh..............hhhhhhhhhhhhhhhheeeee..hhhhh.eeee..hhhhh...........eeee...........eeeeeeee......eeeee.hhhhhhhhhhhhhhh...ee..hhhhhhhhh...hhhhhhhhhhhhhhhhhh.....eeee..eeee..hhh.ee....hhhhhhhhhhhhhhhhhhheee......eeeee...eeeee............eeeeeeee.hhhhhhhhh......ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ne0 A   8 STPSYSLTPAEASAVAELTLELAAAYGSFGDPVLLRDLPRLAARLPEGVQDFLREFKLADRHGHTVIRGHDFDQRRIGPTPDHWRGRVRPGPEFPEELLLMLYSALLGEPFGWATQQDGHLVHDIFPIRSHENDQLGMGSKQLLTWHTEAAFHPYRSDYLILGALRNPDHVPTTVGELDLSSLSAEDIDVLFEPRYHIAPDESHLPKNNTIATEEEAARFATIQRMIDERPLGPLLYGSRLDPYMRLDPYFTSVPQDDTDARRAYDALFKVVDSGMREVVADQGDVLFIDNHRAVHGRLPFQARYDGTDRWLKRVCVTSDLRRSREMRATSATRLLG 344
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       


Chain B from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeee....hhhhhh..............hhhhhhhhhhhhhhhheeeee..hhhhh..eee.......................eeeeeeee.....eeeee..hhhhhhhhhhhhhh....ee...............ee......ee..hhh.ee....hhhhhhhhhhhhhhhhhhheeee.....eeeee....eeee............eeeeeeee.hhhhhhhhh......ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ne0 B   9 TPSYSLTPAEASAVAELTLELAAAYGSFGDPVLLRDLPRLAARLPEGVQDFLREFKLADRHGHTVIRGHDFDQRRIGPTPDHWRGRVRPGPEFPEELLLMLYSALLGEPFGWATQQDGHLVHDIFPIRSHELLTWHTEAAFHPYRSDYLILGALRNPDHVPTTVGELDLSSLSAEDIDVLFEPRYHIAPDESMIDERPLGPLLYGSRLDPYMRLDPYFTSVPQDDTDARRAYDALFKVVDSGMREVVADQGDVLFIDNHRAVHGRLPFQARYDGTDRWLKRVCVTSDLRRSREMRATSATRLLG 344
                                    18        28        38        48        58        68        78        88        98       108       118       128       138||     158       168       178       188       198       208 ||    240       250       260       270       280       290       300       310       320       330       340    
                                                                                                                                                            139|                                                         210|                                                                                                               
                                                                                                                                                             150                                                          233                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:322
                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeee....hhhhhh..............hhhhhhhhhhhhhhhheeeee..hhhhh.eeee..hhhhh...........eeee...........eeeeeeee.....eeeee.......hhhhhhhhh....ee..hhhhh.....hhhhhh.....ee......ee..hhh.ee....hhhhhhhhhhhhhhhhhhheeee.....eeeee....eeee............eeeeeeee.hhhhhhhhh......ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ne0 C   9 TPSYSLTPAEASAVAELTLELAAAYGSFGDPVLLRDLPRLAARLPEGVQDFLREFKLADRHGHTVIRGHDFDQRRIGPTPDHWRGRVRPGPEFPEELLLMLYSALLGEPFGWATQQDGHLVHDIFPIRSHENDQLGMGSKQLLTWHTEAAFHPYRSDYLILGALRNPDHVPTTVGELDLSSLSAEDIDVLFEPRYHIAPDESHLPATIQRMIDERPLGPLLYGSRLDPYMRLDPYFTSVPQDDTDARRAYDALFKVVDSGMREVVADQGDVLFIDNHRAVHGRLPFQARYDGTDRWLKRVCVTSDLRRSREMRATSATRLLG 344
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208    || 232       242       252       262       272       282       292       302       312       322       332       342  
                                                                                                                                                                                                                                      213|                                                                                                                    
                                                                                                                                                                                                                                       228                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeee....hhhhhh..............hhhhhhhhhhhhhhhheeeee..hhhhh.eeee..hhhhh...........eeee...........eeeeeeee......eeee..hhhhhhhhhhhhhh....ee.................eeee..eeee..hhh.ee....hhhhhhhhhhhhhhhhhhheee......eeeee....eeee............eeeeeeee.hhhhhhhhh......ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ne0 D   9 TPSYSLTPAEASAVAELTLELAAAYGSFGDPVLLRDLPRLAARLPEGVQDFLREFKLADRHGHTVIRGHDFDQRRIGPTPDHWRGRVRPGPEFPEELLLMLYSALLGEPFGWATQQDGHLVHDIFPIRSHENDQLGMGSKQLLTWHTEAAFHPYRSDYLILGALRNPDHVPTTVGELDLSSLSAEDIDVLFEPRYHIAPDESHRMIDERPLGPLLYGSRLDPYMRLDPYFTSVPQDDTDARRAYDALFKVVDSGMREVVADQGDVLFIDNHRAVHGRLPFQARYDGTDRWLKRVCVTSDLRRSREMRATSATRLLG 344
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208  ||   238       248       258       268       278       288       298       308       318       328       338      
                                                                                                                                                                                                                                    211|                                                                                                                
                                                                                                                                                                                                                                     232
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4NE0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NE0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NE0)

(-) Gene Ontology  (6, 6)

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        G9MBV2_STRLA | G9MBV2: 4m23 4m25 4m26 4m27 4m2c 4m2e 4m2f 4m2g 4m2i

(-) Related Entries Specified in the PDB File

4m23 4m25 4m26 4m27 4m2c 4m2e 4m2f 4m2g 4m2i 4m2j 4m2k 4m2m