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(-) Description

Title :  STRUCTURE OF PROTOPORPHYRINOGEN OXIDASE FROM MYXOCOCCUS XANTHUS
 
Authors :  H. R. Corradi, A. V. Corrigall, E. Boix, C. G. Mohan, E. D. Sturrock, P. N. Meissner, K. R. Acharya
Date :  13 Jun 06  (Deposition) - 17 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, Protoporphyrinogen Oxidase, Porphyrin Biosynthesis, Chlorophyll Biosynthesis, Fad, Porphyria, Flavoprotein, Heme Biosynthesis, Haem Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. R. Corradi, A. V. Corrigall, E. Boix, C. G. Mohan, E. D. Sturrock, P. N. Meissner, K. R. Acharya
Crystal Structure Of Protoporphyrinogen Oxidase From Myxococcus Xanthus And Its Complex With The Inhibitor Acifluorfen.
J. Biol. Chem. V. 281 38625 2006
PubMed-ID: 17046834  |  Reference-DOI: 10.1074/JBC.M606640200

(-) Compounds

Molecule 1 - PROTOPORPHYRINOGEN OXIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: JM109
    Expression System Taxid: 562
    Organism Scientific: MYXOCOCCUS XANTHUS
    Organism Taxid: 34
    Synonym: PPO, PPOX

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL6Ligand/IonGLYCEROL
3TWN3Ligand/Ion(3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL3Ligand/IonGLYCEROL
3TWN1Ligand/Ion(3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL3Ligand/IonGLYCEROL
3TWN2Ligand/Ion(3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:15 , GLY A:16 , GLY A:18 , ILE A:19 , SER A:20 , LEU A:38 , GLU A:39 , SER A:40 , SER A:41 , GLY A:46 , ALA A:47 , GLY A:61 , PRO A:62 , ASN A:63 , SER A:64 , ALA A:249 , VAL A:251 , ALA A:282 , ALA A:287 , GLY A:440 , ASN A:441 , VAL A:446 , GLY A:447 , LEU A:448 , HOH A:2003 , HOH A:2072 , TWN A:4002BINDING SITE FOR RESIDUE FAD A2114
02AC2SOFTWARETHR A:166 , GLY A:167 , ILE A:168 , ALA A:170 , ILE A:311 , PHE A:329 , GLY A:330 , PHE A:331 , LEU A:332 , GLY A:343 , ALA A:344 , ILE A:345 , MET A:365 , FAD A:2114BINDING SITE FOR RESIDUE TWN A4002
03AC3SOFTWAREVAL B:15 , GLY B:16 , GLY B:18 , ILE B:19 , SER B:20 , LEU B:38 , GLU B:39 , SER B:40 , GLY B:46 , ALA B:47 , GLY B:61 , PRO B:62 , ASN B:63 , SER B:64 , VAL B:251 , ALA B:282 , ALA B:283 , PRO B:284 , ALA B:287 , GLY B:440 , ASN B:441 , GLY B:447 , LEU B:448 , HOH B:2068 , HOH B:2069 , HOH B:2070 , TWN B:4003BINDING SITE FOR RESIDUE FAD B2114
04AC4SOFTWARELEU B:125 , ARG B:126 , GLY B:129 , ARG B:134BINDING SITE FOR RESIDUE TWN B4001
05AC5SOFTWARETHR B:166 , GLY B:167 , ILE B:168 , PHE B:329 , GLY B:330 , PHE B:331 , LEU B:332 , ALA B:344 , ILE B:345 , MET B:365 , FAD B:2114BINDING SITE FOR RESIDUE TWN B4003
06AC6SOFTWAREPRO A:120 , LEU A:121 , GLY A:122 , ALA A:123 , ARG A:201 , HOH A:2073BINDING SITE FOR RESIDUE GOL A3001
07AC7SOFTWAREGLY A:122 , ALA A:123 , ARG A:193 , LEU A:197 , ARG A:201 , HOH A:2026 , HOH A:2043 , HOH A:2074BINDING SITE FOR RESIDUE GOL A3002
08AC8SOFTWAREARG A:126 , GLY A:129BINDING SITE FOR RESIDUE GOL A3003
09AC9SOFTWAREPRO B:120 , GLY B:122 , ARG B:201 , HOH B:2071BINDING SITE FOR RESIDUE GOL B3005
10BC1SOFTWARELEU A:125 , LEU B:125BINDING SITE FOR RESIDUE GOL B3006
11BC2SOFTWAREGLY B:122 , ALA B:123 , ARG B:193 , LEU B:197 , ARG B:201 , HOH B:2032 , HOH B:2072BINDING SITE FOR RESIDUE GOL B3007

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IVE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IVE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IVE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IVE)

(-) Exons   (0, 0)

(no "Exon" information available for 2IVE)

(-) 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:451
 aligned with PPOX_MYXXA | P56601 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:455
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459     
           PPOX_MYXXA    10 MNVAVVGGGISGLAVAHHLRSRGTDAVLLESSARLGGAVGTHALAGYLVEQGPNSFLDREPATRALAAALNLEGRIRAADPAAKRRYVYTRGRLRSVPASPPAFLASDILPLGARLRVAGELFSRRAPEGVDESLAAFGRRHLGHRATQVLLDAVQTGIYAGDVEQLSVAATFPMLVKMEREHRSLILGAIRAQKAQRQAALPAGTAPKLSGALSTFDGGLQVLIDALAASLGDAAHVGARVEGLAREDGGWRLIIEEHGRRAELSVAQVVLAAPAHATAKLLRPLDDALAALVAGIAYAPIAVVHLGFDAGTLPAPDGFGFLVPAEEQRRMLGAIHASTTFPFRAEGGRVLYSCMVGGARQPGLVEQDEDALAALAREELKALAGVTARPSFTRVFRWPLGIPQYNLGHLERVAAIDAALQRLPGLHLIGNAYKGVGLNDCIRNAAQLADALVA 464
               SCOP domains d2ivea1 A:10-306,A:415-464 Protoporphyrinogen oxidase                                                                                                                                                                                                                                                    d2ivea2 A:307-414 Protoporphyrinogen oxidase                                                                d2ivea1 A:10-306,A:415-464                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..hhhhhhhhhhhhh....eeeee..........eeee..eeee.....ee..hhhhhhhhhh..hhh.eee........eeee..eeee...hhhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..----.........eeee...hhhhhhhhhhhhh..eee..eeeeeee....eeeeee....eeeeee.eeee..hhhhhhhhhh..hhhhhhhhhh..eeeeeeeeeee............ee.hhhhh....eeeehhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeeee....hhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ive A  10 MNVAVVGGGISGLAVAHHLRSRGTDAVLLESSARLGGAVGTHALAGYLVEQGPNSFLDREPATRALAAALNLEGRIRAADPAAKRRYVYTRGRLRSVPASPPAFLASDILPLGARLRVAGELFSRRAPEGVDESLAAFGRRHLGHRATQVLLDAVQTGIYAGDVEQLSVAATFPMLVKMEREHRSLILGAIRAQKAQRQA----GTAPKLSGALSTFDGGLQVLIDALAASLGDAAHVGARVEGLAREDGGWRLIIEEHGRRAELSVAQVVLAAPAHATAKLLRPLDDALAALVAGIAYAPIAVVHLGFDAGTLPAPDGFGFLVPAEEQRRMLGAIHASTTFPFRAEGGRVLYSCMVGGARQPGLVEQDEDALAALAREELKALAGVTARPSFTRVFRWPLGIPQYNLGHLERVAAIDAALQRLPGLHLIGNAYKGVGLNDCIRNAAQLADALVA 464
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209    |  219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459     
                                                                                                                                                                                                                                 209  214                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:450
 aligned with PPOX_MYXXA | P56601 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:457
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       
           PPOX_MYXXA    10 MNVAVVGGGISGLAVAHHLRSRGTDAVLLESSARLGGAVGTHALAGYLVEQGPNSFLDREPATRALAAALNLEGRIRAADPAAKRRYVYTRGRLRSVPASPPAFLASDILPLGARLRVAGELFSRRAPEGVDESLAAFGRRHLGHRATQVLLDAVQTGIYAGDVEQLSVAATFPMLVKMEREHRSLILGAIRAQKAQRQAALPAGTAPKLSGALSTFDGGLQVLIDALAASLGDAAHVGARVEGLAREDGGWRLIIEEHGRRAELSVAQVVLAAPAHATAKLLRPLDDALAALVAGIAYAPIAVVHLGFDAGTLPAPDGFGFLVPAEEQRRMLGAIHASTTFPFRAEGGRVLYSCMVGGARQPGLVEQDEDALAALAREELKALAGVTARPSFTRVFRWPLGIPQYNLGHLERVAAIDAALQRLPGLHLIGNAYKGVGLNDCIRNAAQLADALVAGN 466
               SCOP domains d2iveb1 B:10-306,B:415-466 Protoporphyrinogen oxidase                                                                                                                                                                                                                                                    d2iveb2 B:307-414 Protoporphyrinogen oxidase                                                                d2iveb1 B:10-306,B:415-466                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh.eeeeee..........eeee..eeee.....ee..hhhhhhhhhhh.hhh.ee........eeeee..eeeee..hhhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..-------......eeee...hhhhhhhhhhhhh..eee.eeeeeeee....eeeeeee...eeeeee.eeee..hhhhhhhhhh..hhhhhhhhhh..eeeeeeeeeee...........eee.hhhhh....eeeehhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeee....hhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ive B  10 MNVAVVGGGISGLAVAHHLRSRGTDAVLLESSARLGGAVGTHALAGYLVEQGPNSFLDREPATRALAAALNLEGRIRAADPAAKRRYVYTRGRLRSVPASPPAFLASDILPLGARLRVAGELFSRRAPEGVDESLAAFGRRHLGHRATQVLLDAVQTGIYAGDVEQLSVAATFPMLVKMEREHRSLILGAIRAQKAQRQA-------PKLSGALSTFDGGLQVLIDALAASLGDAAHVGARVEGLAREDGGWRLIIEEHGRRAELSVAQVVLAAPAHATAKLLRPLDDALAALVAGIAYAPIAVVHLGFDAGTLPAPDGFGFLVPAEEQRRMLGAIHASTTFPFRAEGGRVLYSCMVGGARQPGLVEQDEDALAALAREELKALAGVTARPSFTRVFRWPLGIPQYNLGHLERVAAIDAALQRLPGLHLIGNAYKGVGLNDCIRNAAQLADALVAGN 466
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       
                                                                                                                                                                                                                                 209     217
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2IVE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IVE)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PPOX_MYXXA | P56601)
molecular function
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004729    oxygen-dependent protoporphyrinogen oxidase activity    Catalysis of the reaction: 3 O(2) + protoporphyrinogen IX = 3 H(2)O(2) + protoporphyrin IX.
biological process
    GO:0006783    heme biosynthetic process    The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006779    porphyrin-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
    GO:0006782    protoporphyrinogen IX biosynthetic process    The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PPOX_MYXXA | P56601: 2ivd

(-) Related Entries Specified in the PDB File

2ivd STRUCTURE OF PROTOPORPHYRINOGEN OXIDASE FROM MYXOCOCCUS XANTHUS WITH ACIFLUORFEN