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(-) Description

Title :  CRYSTAL STRUCTURE OF NON-HEME IRON OXYGENASE ORFP IN COMPLEX WITH FE, SUCCINATE, AND (3R,4R)-DIHYDROXY-L-ARG
 
Authors :  C. Y. Chang, Y. C. Liu, S. Y. Lyu, C. C. Wu, T. L. Li
Date :  05 Aug 13  (Deposition) - 25 Jun 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hydroxylase, Fe Binding, Oxidoreductase (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
    Organism Scientific: STREPTOMYCES LAVENDULAE
    Organism Taxid: 58340
    Synonym: 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, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
12OR2Ligand/IonAMINO{[(2R,3R,4S)-4-AMINO-2,3,5-TRIHYDROXY-5-OXOPENTYL]AMINO}METHANIMINIUM
2FE4Ligand/IonFE (III) ION
3SIN4Ligand/IonSUCCINIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
12OR-1Ligand/IonAMINO{[(2R,3R,4S)-4-AMINO-2,3,5-TRIHYDROXY-5-OXOPENTYL]AMINO}METHANIMINIUM
2FE-1Ligand/IonFE (III) ION
3SIN2Ligand/IonSUCCINIC ACID
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
12OR2Ligand/IonAMINO{[(2R,3R,4S)-4-AMINO-2,3,5-TRIHYDROXY-5-OXOPENTYL]AMINO}METHANIMINIUM
2FE-1Ligand/IonFE (III) ION
3SIN2Ligand/IonSUCCINIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:154 , GLU A:156 , HIS A:303 , SIN A:402 , HOH A:617BINDING SITE FOR RESIDUE FE A 401
02AC2SOFTWAREILE A:132 , GLY A:144 , LEU A:151 , THR A:180 , HIS A:303 , ARG A:305 , ARG A:317 , FE A:401BINDING SITE FOR RESIDUE SIN A 402
03AC3SOFTWAREHIS B:154 , GLU B:156 , HIS B:303 , ARG B:321BINDING SITE FOR RESIDUE FE B 401
04AC4SOFTWAREILE B:132 , THR B:180 , HIS B:303 , ARG B:317 , ARG B:321 , HOH B:568BINDING SITE FOR RESIDUE SIN B 402
05AC5SOFTWAREHIS C:154 , GLU C:156 , HIS C:303 , ARG C:321 , 2OR C:402 , SIN C:403BINDING SITE FOR RESIDUE FE C 401
06AC6SOFTWAREGLN C:123 , 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:401 , SIN C:403BINDING SITE FOR RESIDUE 2OR C 402
07AC7SOFTWARELEU C:151 , THR C:180 , HIS C:303 , ARG C:317 , ARG C:321 , FE C:401 , 2OR C:402BINDING SITE FOR RESIDUE SIN C 403
08AC8SOFTWAREHIS D:154 , GLU D:156 , HIS D:303 , 2OR D:402 , SIN D:403BINDING SITE FOR RESIDUE FE D 401
09AC9SOFTWAREGLN D:123 , GLN D:142 , LEU D:143 , GLY D:144 , HIS D:154 , GLU D:156 , ASP D:208 , SER D:210 , ASP D:255 , PHE D:258 , ARG D:321 , FE D:401 , SIN D:403BINDING SITE FOR RESIDUE 2OR D 402
10BC1SOFTWAREGLY D:144 , THR D:180 , HIS D:303 , ARG D:317 , FE D:401 , 2OR D:402BINDING SITE FOR RESIDUE SIN D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M2G)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:96 -Pro A:97
2Arg B:96 -Pro B:97
3Arg C:96 -Pro C:97
4Arg D:96 -Pro D:97

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M2G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M2G)

(-) Exons   (0, 0)

(no "Exon" information available for 4M2G)

(-) 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:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeee....hhhhhh..............hhhhhhhhhhhhhhhheeeee.hhhhhh..eee..hhhhh...........eeee...........eeeeeeee......eeeee.hhhhhhhhhhhhhh....ee..hhhhh......hhhhhhh.hhhhhhhhhhh.....ee......ee..hhh.ee....hhhhhhhhhhhhhhhhhhheee.....eeeeee...eeeee............eeeeeeee.hhhhhhhhh......ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4m2g A   9 TPSYSLTPAEASAVAELTLELAAAYGSFGDPVLLRDLPRLAARLPEGVQDFLREFKLADRHGHTVIRGHDFDQRRIGPTPDHWRGRVRPGPEFPEELLLMLYSALLGEPFGWATQQDGHLVHDIFPIRSHENDQLGMGSKQLLTWHTEDAFHPYRSDYLILGALRNPDHVPTTVGELDLSSLSAEDIDVLFEPRYHIAPDESHLPKNNTIATEEEAARFATIQRMIDERPLGPLLYGSRLDPYMRLDPYFTSVPQDDTDARRAYDALFKVVDSGMREVVADQGDVLFIDNHRAVHGRLPFQARYDGTDRWLKRVCVTSDLRRSREMRATSATRLLG 344
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338      


Chain B from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeee....hhhhhh..............hhhhhhhhhhhhhhhheeeee.hhhhhh..eee.........................eeeeeeee......eeee.......hhhhhhhhh...eee..............ee..eee....eee..hhh.ee....hhhhhhhhhhhhhhhhhhheee......eeeee....eeee............eeeeeeee.hhhhhhhhh......ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m2g B   9 TPSYSLTPAEASAVAELTLELAAAYGSFGDPVLLRDLPRLAARLPEGVQDFLREFKLADRHGHTVIRGHDFDQRRIGPTPDHWRGRVRPGPEFPEELLLMLYSALLGEPFGWATQQDGHLVHDIFPIRSHEKQLLTWHTEDAFHPYRSDYLILGALRNPDHVPTTVGELDLSSLSAEDIDVLFEPRYHIAPDESIQRMIDERPLGPLLYGSRLDPYMRLDPYFTSVPQDDTDARRAYDALFKVVDSGMREVVADQGDVLFIDNHRAVHGRLPFQARYDGTDRWLKRVCVTSDLRRSREMRATSATRLLG 344
                                    18        28        38        48        58        68        78        88        98       108       118       128       138||     156       166       176       186       196       206   ||  235       245       255       265       275       285       295       305       315       325       335         
                                                                                                                                                            139|                                                           210|                                                                                                                  
                                                                                                                                                             148                                                            230                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeee....hhhhhh..............hhhhhhhhhhhhhhhheeeee.hhhhhh.eeee..hhhhh...........eeee...........eeeeeeee.....eeeee.......hhhhhhhhh....ee..hhhhh............hhhhhhhh.....eeee..eeee..hhh.ee....hhhhhhhhhhhhhhhhhh.eeee.....eeeee....eeee............eeeeeeee.hhhhhhhhh......ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m2g C   9 TPSYSLTPAEASAVAELTLELAAAYGSFGDPVLLRDLPRLAARLPEGVQDFLREFKLADRHGHTVIRGHDFDQRRIGPTPDHWRGRVRPGPEFPEELLLMLYSALLGEPFGWATQQDGHLVHDIFPIRSHENDQLGMGSKQLLTWHTEDAFHPYRSDYLILGALRNPDHVPTTVGELDLSSLSAEDIDVLFEPRYHIAPDESHLPKNNTIAARFATIQRMIDERPLGPLLYGSRLDPYMRLDPYFTSVPQDDTDARRAYDALFKVVDSGMREVVADQGDVLFIDNHRAVHGRLPFQARYDGTDRWLKRVCVTSDLRRSREMRATSATRLLG 344
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218|      233       243       253       263       273       283       293       303       313       323       333       343 
                                                                                                                                                                                                                                           218|                                                                                                                        
                                                                                                                                                                                                                                            224                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhh...eeeee....hhhhhh..............hhhhhhhhhhhhhhhheeeee..hhhhh..eee..................eeee...........eeeeeeee.....eeeee..hhhhhhhhhhhhhh....ee......hhhhh............hhhhhhhhh.....eeee..eeee..hhh.ee....hhhhhhhhhhhhhhhhhhheeee.....eeeee....eeee............eeeeeeee.hhhhhhhhh......ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4m2g D   9 TPSYSLTPAEASAVAELTLELAAAYGSFGDPVLLRDLPRLAARLPEGVQDFLREFKLADRHGHTVIRGHDFDQRRIGPTPDHWRGRVRPGPEFPEELLLMLYSALLGEPFGWATQQDGHLVHDIFPIRSHENDQLGMGSKQLLTWHTEDAFHPYRSDYLILGALRNPDHVPTTVGELDLSSLSAEDIDVLFEPRYHIAPDESHLPKNNTIATEEEAARFATIQRMIDERPLGPLLYGSRLDPYMRLDPYFTSVPQDDTDARRAYDALFKVVDSGMREVVADQGDVLFIDNHRAVHGRLPFQARYDGTDRWLKRVCVTSDLRRSREMRATSATRLLG 344
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338
   Legend:   → Mismatch (orange background)
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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 4M2G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M2G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M2G)

(-) Gene Ontology  (6, 6)

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 Related Entries

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        G9MBV2_STRLA | G9MBV2: 4m23 4m25 4m26 4m27 4m2c 4m2e 4m2f 4m2i 4ne0

(-) Related Entries Specified in the PDB File

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