2IVD - JenaLib

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Title :   STRUCTURE OF PROTOPORPHYRINOGEN OXIDASE FROM MYXOCOCCUS XANTHUS WITH ACIFLUORFEN

Authors :   H. R. Corradi, A. V. Corrigall, E. Boix, C. G. Mohan, E. D. Sturrock, P. N. Meissner, K. R. Acharya

Date :   12 Jun 06 (Deposition) - 17 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Protoporphyrinogen Oxidase, Porphyrin Biosynthesis, Chlorophyll Biosynthesis, Oxidoreductase, Haem Biosynthesis, Heme Biosynthesis, Fad, Porphyria, Acifluorfen, Flavoprotein (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

Molecule 1 - PROTOPORPHYRINOGEN OXIDASE
	Chains	:	A, B
	EC Number	:	1.3.3.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Organism Scientific	:	MYXOCOCCUS XANTHUS
	Organism Taxid	:	34
	Synonym	:	PPO, PPOX

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	ACJ	2	Ligand/Ion	5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHENOXY]-2-NITROBENZOIC ACID
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	GOL	5	Ligand/Ion	GLYCEROL
4	TWN	1	Ligand/Ion	(3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	ACJ	1	Ligand/Ion	5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHENOXY]-2-NITROBENZOIC ACID
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	GOL	2	Ligand/Ion	GLYCEROL
4	TWN	-1	Ligand/Ion	(3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE

Biological Unit 2 (4, 6)

No.	Name	Count	Type	Full Name
1	ACJ	1	Ligand/Ion	5-[2-CHLORO-4-(TRIFLUOROMETHYL)PHENOXY]-2-NITROBENZOIC ACID
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	GOL	3	Ligand/Ion	GLYCEROL
4	TWN	1	Ligand/Ion	(3S)-3-[(2S,3S,4R)-3,4-DIMETHYLTETRAHYDROFURAN-2-YL]BUTYL LAURATE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:95 , THR A:166 , GLY A:167 , ILE A:168 , TYR A:169 , ALA A:170 , ILE A:311 , PHE A:329 , GLY A:330 , PHE A:331 , LEU A:332 , MET A:365 , ILE A:412 , FAD A:1466 , HOH A:2068	BINDING SITE FOR RESIDUE ACJ A1465
02	AC2	SOFTWARE	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 , ARG A:250 , VAL A:251 , ALA A:282 , ALA A:283 , ALA A:287 , ILE A:412 , GLY A:440 , ASN A:441 , VAL A:446 , GLY A:447 , LEU A:448 , ACJ A:1465 , HOH A:2008 , HOH A:2016 , HOH A:2141 , HOH A:2142 , HOH A:2143 , HOH A:2144 , HOH A:2145	BINDING SITE FOR RESIDUE FAD A1466
03	AC3	SOFTWARE	ARG B:95 , THR B:166 , GLY B:167 , ILE B:168 , TYR B:169 , ALA B:170 , ILE B:311 , PHE B:329 , GLY B:330 , PHE B:331 , LEU B:332 , ALA B:344 , ILE B:345 , MET B:365 , ILE B:412 , FAD B:1469 , HOH B:2132	BINDING SITE FOR RESIDUE ACJ B1468
04	AC4	SOFTWARE	VAL 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:283 , PRO B:284 , ALA B:287 , VAL B:313 , GLY B:440 , ASN B:441 , VAL B:446 , GLY B:447 , LEU B:448 , ACJ B:1468 , HOH B:2001 , HOH B:2129 , HOH B:2133 , HOH B:2134 , HOH B:2136 , HOH B:2137	BINDING SITE FOR RESIDUE FAD B1469
05	AC5	SOFTWARE	LEU B:125 , ARG B:126 , GLY B:129 , ARG B:134 , GOL B:1467 , HOH B:2131 , HOH B:2142	BINDING SITE FOR RESIDUE TWN B1472
06	AC6	SOFTWARE	PRO A:120 , LEU A:121 , GLY A:122 , ALA A:123 , ARG A:201 , HOH A:2146	BINDING SITE FOR RESIDUE GOL A1467
07	AC7	SOFTWARE	GLY A:122 , ALA A:123 , ARG A:155 , HIS A:192 , ARG A:193 , LEU A:197 , ARG A:201 , HOH A:2063	BINDING SITE FOR RESIDUE GOL A1468
08	AC8	SOFTWARE	ARG B:126 , ARG B:193 , TWN B:1472 , HOH B:2045 , HOH B:2131	BINDING SITE FOR RESIDUE GOL B1467
09	AC9	SOFTWARE	PRO B:120 , LEU B:121 , GLY B:122 , ALA B:123 , ARG B:201 , HOH B:2138	BINDING SITE FOR RESIDUE GOL B1470
10	BC1	SOFTWARE	GLY B:122 , ALA B:123 , ARG B:193 , LEU B:197 , ARG B:201 , HOH B:2072 , HOH B:2140 , HOH B:2141	BINDING SITE FOR RESIDUE GOL B1471

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

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

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

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

(no "Exon" information available for 2IVD)

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:449
 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 d2ivda1 A:10-306,A:415-464 Protoporphyrinogen oxidase                                                                                                                                                                                                                                                    d2ivda2 A:307-414 Protoporphyrinogen oxidase                                                                d2ivda1 A:10-306,A:415-464                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..hhhhhhhhhhhhh....eeee...........eeee..eeee.....ee..hhhhhhhhhhh.hhh.ee........eeeee..eeee...hhhhhhh....hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..----.........eeee...hhhhhhhhhhhhh..ee..eeeeeee..--..eeeeee..eeeeee..eeee..hhhhhhhhhh..hhhhhhhhhh.....eeeeeeee...........eee.hhhhh....eeeehhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.........hhhhhhhhhhhhhhh...eee........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ivd A  10 MNVAVVGGGISGLAVAHHLRSRGTDAVLLESSARLGGAVGTHALAGYLVEQGPNSFLDREPATRALAAALNLEGRIRAADPAAKRRYVYTRGRLRSVPASPPAFLASDILPLGARLRVAGELFSRRAPEGVDESLAAFGRRHLGHRATQVLLDAVQTGIYAGDVEQLSVAATFPMLVKMEREHRSLILGAIRAQKAQRQA----GTAPKLSGALSTFDGGLQVLIDALAASLGDAAHVGARVEGLARE--GWRLIIEEHGRRAELSVAQVVLAAPAHATAKLLRPLDDALAALVAGIAYAPIAVVHLGFDAGTLPAPDGFGFLVPAEEQRRMLGAIHASTTFPFRAEGGRVLYSCMVGGARQPGLVEQDEDALAALAREELKALAGVTARPSFTRVFRWPLGIPQYNLGHLERVAAIDAALQRLPGLHLIGNAYKGVGLNDCIRNAAQLADALVA 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       | -|      269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459     
                                                                                                                                                                                                                                 209  214                                        257  |                                                                                                                                                                                                            
                                                                                                                                                                                                                                                                                    260

Chain B from PDB  Type:PROTEIN  Length:449
 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 d2ivdb1 B:10-306,B:415-466 Protoporphyrinogen oxidase                                                                                                                                                                                                                                                    d2ivdb2 B:307-414 Protoporphyrinogen oxidase                                                                d2ivdb1 B:10-306,B:415-466                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeee...........eeee..eeee.....ee..hhhhhhhhhhh.hhh.eee........eee....eee...hhhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.--------.....eeee...hhhhhhhhhhhhh..ee...eeeeeee....eeeeeee..eeeeeee.eeee..hhhhhhhhhh..hhhhhhhhhh.eeeeeeeeeeee...........eee.hhhhh....eeeehhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeee...hhhhhhhhhhhhhhh...eee........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ivd B  10 MNVAVVGGGISGLAVAHHLRSRGTDAVLLESSARLGGAVGTHALAGYLVEQGPNSFLDREPATRALAAALNLEGRIRAADPAAKRRYVYTRGRLRSVPASPPAFLASDILPLGARLRVAGELFSRRAPEGVDESLAAFGRRHLGHRATQVLLDAVQTGIYAGDVEQLSVAATFPMLVKMEREHRSLILGAIRAQKAQRQA--------KLSGALSTFDGGLQVLIDALAASLGDAAHVGARVEGLAREDGGWRLIIEEHGRRAELSVAQVVLAAPAHATAKLLRPLDDALAALVAGIAYAPIAVVHLGFDAGTLPAPDGFGFLVPAEEQRRMLGAIHASTTFPFRAEGGRVLYSCMVGGARQPGLVEQDEDALAALAREELKALAGVTARPSFTRVFRWPLGIPQYNLGHLERVAAIDAALQRLPGLHLIGNAYKGVGLNDCIRNAAQLADALVAGN 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      218

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

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

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

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.

Asymmetric Unit
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	PPOX_MYXXA \| P56601	:	2ive

2ive	STRUCTURE OF PROTOPORPHYRINOGEN OXIDASE FROM MYXOCOCCUS XANTHUS

Description

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Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

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