1SEZ - JenaLib

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Title :   CRYSTAL STRUCTURE OF PROTOPORPHYRINOGEN IX OXIDASE

Authors :   M. Koch, C. Breithaupt, R. Kiefersauer, J. Freigang, R. Huber, A. Messerschmidt

Date :   19 Feb 04 (Deposition) - 13 Apr 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Fad-Binding, Para-Hydroxy-Benzoate-Hydroxylase Fold (Phbh- Fold), Monotopic Membrane-Binding Domain, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Koch, C. Breithaupt, R. Kiefersauer, J. Freigang, R. Huber, A. Messerschmidt
Crystal Structure Of Protoporphyrinogen Ix Oxidase: A Key Enzyme In Haem And Chlorophyll Biosynthesis.
Embo J. V. 23 1720 2004
PubMed-ID: 15057273 | Reference-DOI: 10.1038/SJ.EMBOJ.7600189
(for further references see the PDB file header)

Molecule 1 - PROTOPORPHYRINOGEN OXIDASE, MITOCHONDRIAL
	Chains	:	A, B
	EC Number	:	1.3.3.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET32A-PPO2NT
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PPXII, PPOX2
	Organism Common	:	COMMON TOBACCO
	Organism Scientific	:	NICOTIANA TABACUM
	Organism Taxid	:	4097
	Synonym	:	PPO II, PROTOPORPHYRINOGEN IX OXIDASE ISOZYME II, PPX II, PX-2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 24)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
3	OMN	2	Ligand/Ion	4-BROMO-3-(5'-CARBOXY-4'-CHLORO-2'-FLUOROPHENYL)-1-METHYL-5-TRIFLUOROMETHYL-PYRAZOL
4	TON	2	Ligand/Ion	2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL

Biological Unit 1 (4, 24)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE
3	OMN	2	Ligand/Ion	4-BROMO-3-(5'-CARBOXY-4'-CHLORO-2'-FLUOROPHENYL)-1-METHYL-5-TRIFLUOROMETHYL-PYRAZOL
4	TON	2	Ligand/Ion	2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL

Biological Unit 2 (4, 48)

No.	Name	Count	Type	Full Name
1	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	MSE	36	Mod. Amino Acid	SELENOMETHIONINE
3	OMN	4	Ligand/Ion	4-BROMO-3-(5'-CARBOXY-4'-CHLORO-2'-FLUOROPHENYL)-1-METHYL-5-TRIFLUOROMETHYL-PYRAZOL
4	TON	4	Ligand/Ion	2-{2-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENOXY]ETHOXY}ETHANOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:19 , GLY A:20 , GLY A:22 , VAL A:23 , SER A:24 , PHE A:42 , GLU A:43 , ALA A:44 , GLY A:50 , LYS A:51 , GLY A:65 , ALA A:66 , ASN A:67 , THR A:68 , ARG A:263 , VAL A:264 , ALA A:304 , ASP A:308 , VAL A:336 , ALA A:438 , PHE A:439 , ASN A:468 , SER A:474 , VAL A:475 , OMN A:601 , HOH A:608	BINDING SITE FOR RESIDUE FAD A 600
2	AC2	SOFTWARE	GLY B:20 , GLY B:22 , VAL B:23 , SER B:24 , PHE B:42 , GLU B:43 , ALA B:44 , GLY B:50 , LYS B:51 , GLY B:65 , ALA B:66 , ASN B:67 , THR B:68 , ARG B:263 , VAL B:264 , ALA B:304 , ASP B:308 , ALA B:438 , PHE B:439 , ASN B:468 , SER B:474 , VAL B:475 , OMN B:604 , HOH B:618	BINDING SITE FOR RESIDUE FAD B 610
3	AC3	SOFTWARE	ARG A:98 , ALA A:174 , GLY A:175 , CYS A:177 , GLY A:178 , LEU A:334 , GLY A:354 , LEU A:356 , LEU A:369 , GLY A:370 , THR A:371 , LEU A:372 , PHE A:392 , FAD A:600	BINDING SITE FOR RESIDUE OMN A 601
4	AC4	SOFTWARE	LEU A:109 , LEU A:168 , PHE A:172 , LEU A:356	BINDING SITE FOR RESIDUE TON A 603
5	AC5	SOFTWARE	ARG B:98 , ALA B:174 , GLY B:175 , CYS B:177 , GLY B:178 , LEU B:334 , GLY B:354 , VAL B:355 , LEU B:356 , LEU B:369 , GLY B:370 , THR B:371 , PHE B:392 , TON B:605 , FAD B:610	BINDING SITE FOR RESIDUE OMN B 604
6	AC6	SOFTWARE	LEU B:109 , LEU B:168 , PHE B:172 , PHE B:190 , LEU B:356 , OMN B:604 , HOH B:621	BINDING SITE FOR RESIDUE TON B 605

(no "SS Bond" information available for 1SEZ)

(no "Cis Peptide Bond" information available for 1SEZ)

(no "SAP(SNP)/Variant" information available for 1SEZ)

(no "PROSITE Motif" information available for 1SEZ)

(no "Exon" information available for 1SEZ)

Asymmetric Unit

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	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:465
 aligned with PPOM_TOBAC | O24164 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:485
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492     
           PPOM_TOBAC    13 AKRVAVIGAGVSGLAAAYKLKIHGLNVTVFEAEGKAGGKLRSVSQDGLIWDEGANTMTESEGDVTFLIDSLGLREKQQFPLSQNKRYIARNGTPVLLPSNPIDLIKSNFLSTGSKLQMLLEPILWKNKKLSQVSDSHESVSGFFQRHFGKEVVDYLIDPFVAGTCGGDPDSLSMHHSFPELWNLEKRFGSVILGAIRSKLSPKNEKKQGPPKTSANKKRQRGSFSFLGGMQTLTDAICKDLREDELRLNSRVLELSCSCTEDSAIDSWSIISASPHKRQSEEESFDAVIMTAPLCDVKSMKIAKRGNPFLLNFIPEVDYVPLSVVITTFKRENVKYPLEGFGVLVPSKEQQHGLKTLGTLFSSMMFPDRAPNNVYLYTTFVGGSRNRELAKASRTELKEIVTSDLKQLLGAEGEPTYVNHLYWSKAFPLYGHNYDSVLDAIDKMEKNLPGLFYAGNHRGGLSVGKALSSGCNAADLVISYLESVS 497
               SCOP domains d1seza1 A:13-329,A:442-497 Protoporphyrinogen oxidase                                                                                                                                                                                                                                                                        d1seza2 A:330-441 Protoporphyrinogen oxidase                                                                    d1seza1 A:13-329,A:442-497 Protoporphyrinogen oxidase    SCOP domains
               CATH domains 1sezA01 A:13-50,A:244-330,A:443-497   1sezA02 A:51-108,A:225-240,A:331-441                      1sezA03 A:109-136,A:150-213 -------------1sezA03 A:109-136,A:150-213                                     -----------1sezA02         ---1sezA01 A:13-50,A:244-330,A:443-497  [code=3.50.50.60, no name defined]                1sezA02 A:51-108,A:225-240,A:331-441 Protoporphyrinogen oxidase, mitochondrial; domain 2                       -1sezA01 A:13-50,A:244-330,A:443-497                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhh...eeeee...........eeee..eeee.........hhhhhhhhhhh.hhh.ee.......eeee....eee...hhhhhhhh...hhhhhhhhhhhhhhh----------...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh..----------.............ee...hhhhhhhhhh......ee....eeeeeee........eeeeee...........ee.eeee..hhhhhhh.eee...............eeeeeeeeeeee.hhh.......eee.hhhhhhhh....eeeehhhhhhhhh...eeeeeeeee...hhhhh..hhhhhhhhhhhhhhhhhh.......eeeeeeeeeee....hhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sez A  13 AKRVAVIGAGVSGLAAAYKLKIHGLNVTVFEAEGKAGGKLRSVSQDGLIWDEGANTmTESEGDVTFLIDSLGLREKQQFPLSQNKRYIARNGTPVLLPSNPIDLIKSNFLSTGSKLQmLLEPILW----------SHESVSGFFQRHFGKEVVDYLIDPFVAGTCGGDPDSLSmHHSFPELWNLEKRFGSVILGAIRSKLS----------KTSANKKRQRGSFSFLGGmQTLTDAICKDLREDELRLNSRVLELSCSCTEDSAIDSWSIISASPHKRQSEEESFDAVImTAPLCDVKSmKIAKRGNPFLLNFIPEVDYVPLSVVITTFKRENVKYPLEGFGVLVPSKEQQHGLKTLGTLFSSmmFPDRAPNNVYLYTTFVGGSRNRELAKASRTELKEIVTSDLKQLLGAEGEPTYVNHLYWSKAFPLYGHNYDSVLDAIDKmEKNLPGLFYAGNHRGGLSVGKALSSGCNAADLVISYLESVS 497
                                    22        32        42        52        62      | 72        82        92       102       112       122       132    |    -     | 152       162       172       182   |   192       202       212|        - |     232       242       252       262       272       282       292       302       312       322       332       342       352       362       372   ||  382       392       402       412       422       432       442       452   |   462       472       482       492     
                                                                                   69-MSE                                                      130-MSE137        148                                   186-MSE                    213        224               242-MSE                                                     302-MSE   312-MSE                                                         376-MSE                                                                         456-MSE                                     
                                                                                                                                                                                                                                                                                                                                                                                                      377-MSE

Chain B from PDB  Type:PROTEIN  Length:465
 aligned with PPOM_TOBAC | O24164 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:485
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492     
           PPOM_TOBAC    13 AKRVAVIGAGVSGLAAAYKLKIHGLNVTVFEAEGKAGGKLRSVSQDGLIWDEGANTMTESEGDVTFLIDSLGLREKQQFPLSQNKRYIARNGTPVLLPSNPIDLIKSNFLSTGSKLQMLLEPILWKNKKLSQVSDSHESVSGFFQRHFGKEVVDYLIDPFVAGTCGGDPDSLSMHHSFPELWNLEKRFGSVILGAIRSKLSPKNEKKQGPPKTSANKKRQRGSFSFLGGMQTLTDAICKDLREDELRLNSRVLELSCSCTEDSAIDSWSIISASPHKRQSEEESFDAVIMTAPLCDVKSMKIAKRGNPFLLNFIPEVDYVPLSVVITTFKRENVKYPLEGFGVLVPSKEQQHGLKTLGTLFSSMMFPDRAPNNVYLYTTFVGGSRNRELAKASRTELKEIVTSDLKQLLGAEGEPTYVNHLYWSKAFPLYGHNYDSVLDAIDKMEKNLPGLFYAGNHRGGLSVGKALSSGCNAADLVISYLESVS 497
               SCOP domains d1sezb1 B:13-329,B:442-497 Protoporphyrinogen oxidase                                                                                                                                                                                                                                                                        d1sezb2 B:330-441 Protoporphyrinogen oxidase                                                                    d1sezb1 B:13-329,B:442-497 Protoporphyrinogen oxidase    SCOP domains
               CATH domains 1sezB01 B:13-50,B:244-330,B:443-497   1sezB02 B:51-108,B:225-240,B:331-441                      1sezB03 B:109-136,B:150-213 -------------1sezB03 B:109-136,B:150-213                                     -----------1sezB02         ---1sezB01 B:13-50,B:244-330,B:443-497  [code=3.50.50.60, no name defined]                1sezB02 B:51-108,B:225-240,B:331-441 Protoporphyrinogen oxidase, mitochondrial; domain 2                       -1sezB01 B:13-50,B:244-330,B:443-497                     CATH domains
           Pfam domains (1) ----------Amino_oxidase-1sezB01 B:23-490                                                                                                                                                                                                                                                                                                                                                                                                                                                      ------- Pfam domains (1)
           Pfam domains (2) ----------Amino_oxidase-1sezB02 B:23-490                                                                                                                                                                                                                                                                                                                                                                                                                                                      ------- Pfam domains (2)
         Sec.struct. author ..eeeee..hhhhhhhhhhhhh...eeeeee..........ee......ee.........hhhhhhhhhhh.hhh.ee.......eeeee..eeee..............hhhhhhhhhhhhhhh----------...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhh....----------...hhhhhhh...ee...hhhhhhhhhh......eee...eeeee............eeee..............eeee..hhhhhh..eee...............eeeeeeeeeeee.hhh.......eee.hhhhhhhh....eeeehhhhhhhhh...eeeeeeeee...hhhhh..hhhhhhhhhhhhhhhhhh.......eeeeeeeeeee....hhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sez B  13 AKRVAVIGAGVSGLAAAYKLKIHGLNVTVFEAEGKAGGKLRSVSQDGLIWDEGANTmTESEGDVTFLIDSLGLREKQQFPLSQNKRYIARNGTPVLLPSNPIDLIKSNFLSTGSKLQmLLEPILW----------SHESVSGFFQRHFGKEVVDYLIDPFVAGTCGGDPDSLSmHHSFPELWNLEKRFGSVILGAIRSKLS----------KTSANKKRQRGSFSFLGGmQTLTDAICKDLREDELRLNSRVLELSCSCTEDSAIDSWSIISASPHKRQSEEESFDAVImTAPLCDVKSmKIAKRGNPFLLNFIPEVDYVPLSVVITTFKRENVKYPLEGFGVLVPSKEQQHGLKTLGTLFSSmmFPDRAPNNVYLYTTFVGGSRNRELAKASRTELKEIVTSDLKQLLGAEGEPTYVNHLYWSKAFPLYGHNYDSVLDAIDKmEKNLPGLFYAGNHRGGLSVGKALSSGCNAADLVISYLESVS 497
                                    22        32        42        52        62      | 72        82        92       102       112       122       132    |    -     | 152       162       172       182   |   192       202       212|        - |     232       242       252       262       272       282       292       302       312       322       332       342       352       362       372   ||  382       392       402       412       422       432       442       452   |   462       472       482       492     
                                                                                   69-MSE                                                      130-MSE137        148                                   186-MSE                    213        224               242-MSE                                                     302-MSE   312-MSE                                                         376-MSE                                                                         456-MSE                                     
                                                                                                                                                                                                                                                                                                                                                                                                      377-MSE

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Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(bba) Sandwich (528)

Topology: FAD/NAD(P)-binding domain (373)

Homologous Superfamily: [code=3.50.50.60, no name defined] (373)

Common tobacco (Nicotiana tabacum) (1)

1a	1sezA01	A:13-50,A:244-330,A:443-497
1b	1sezB01	B:13-50,B:244-330,B:443-497

Architecture: Alpha-Beta Complex (3881)

Topology: Polyamine Oxidase; Chain A, domain 2 (62)

Homologous Superfamily: Protoporphyrinogen oxidase, mitochondrial; domain 2 (1)

Common tobacco (Nicotiana tabacum) (1)

2a	1sezA02	A:51-108,A:225-240,A:331-441
2b	1sezB02	B:51-108,B:225-240,B:331-441

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: protoporphyrinogen ix oxidase, domain 3 (1)

Homologous Superfamily: protoporphyrinogen ix oxidase, domain 3 (1)

Common tobacco (Nicotiana tabacum) (1)

3a	1sezA03	A:109-136,A:150-213
3b	1sezB03	B:109-136,B:150-213

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: Amino_oxidase (60)

Nicotiana tabacum (Common tobacco) (1)

1a	Amino_oxidase-1sezB01	B:23-490
1b	Amino_oxidase-1sezB02	B:23-490

Asymmetric Unit(hide GO term definitions)

Chain A,B (PPOM_TOBAC | O24164)

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:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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Description

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Ligands, Modified Residues, Ions (4, 24)

Sites (6, 6)

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