1VJU - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   COPROPORPHYRINOGEN III OXIDASE FROM LEISHMANIA MAJOR

Authors :   Structural Genomics Of Pathogenic Protozoa Consortium (Sgpp)

Date :   29 Mar 04 (Deposition) - 13 Apr 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Structural Genomics, Psi, Protein Structure Initiative, Structural Genomics Of Pathogenic Protozoa Consortium, Sgpp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Structural Genomics Of Pathogenic Protozoa
Coproporphyrinogen Iii Oxidase From Leishmania Major
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - COPROPORPHYRINOGEN III OXIDASE
	Chains	:	A, B
	EC Number	:	1.3.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3A
	Expression System Taxid	:	562
	Expression System Vector	:	PLASMID
	Organism Scientific	:	LEISHMANIA MAJOR
	Organism Taxid	:	5664

		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 (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1VJU)

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPROGEN_OXIDASE	PS01021	Coproporphyrinogen III oxidase signature.	HEM6_LEIMA	165-189	2	A:173-197 B:173-197

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPROGEN_OXIDASE	PS01021	Coproporphyrinogen III oxidase signature.	HEM6_LEIMA	165-189	1	A:173-197 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPROGEN_OXIDASE	PS01021	Coproporphyrinogen III oxidase signature.	HEM6_LEIMA	165-189	1	- B:173-197

(no "Exon" information available for 1VJU)

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:291
 aligned with HEM6_LEIMA | P84155 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:302
                             1                                                                                                                                                                                                                                                                                                            
                             |       9        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  
           HEM6_LEIMA     - -MSLAVEAVKDFLLKLQDDICEALEAEDGQATFVEDKWTREGGGGGRTRVMVDGAVIEKGGVNFSHVYGKGLPMSSTERHPDIAGCNFEAMGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRDFHQVAQDLCKPFGADVYARFKGWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYMDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYNWQPEPGTPEARLTEYFLTKRQWV 301
               SCOP domains d1vjua_ A: Hypothetical protein Lmaj006828                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1vjuA00 A:8-309 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee...eeeeeeeee....eeeeeeeeeeeeee.-----------....eeeeeeeeeeeee......eeeeeeeeeeeee..eeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhheehhhhee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...............hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------COPROGEN_OXIDASE         ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vju A   8 HmSLAVEAVKDFLLKLQDDICEALEAEDGQATFVEDKWTREGGGGGRTRVmVDGAVIEKGGVNFSHVYGKG-----------IAGCNFEAmGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRDFHQVAQDLCKPFGADVYARFKGWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYmDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYNWQPEPGTPEARLTEYFLTKRQWV 309
                             |      17        27        37        47        57|       67        77|        -  |     97|      107       117       127       137       147       157       167       177       187       197       207       217 |     227       237       247       257       267       277       287       297       307  
                             |                                               58-MSE              78          90      98-MSE                                                                                                                  219-MSE                                                                                      
                             9-MSE

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with HEM6_LEIMA | P84155 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:304
                               1                                                                                                                                                                                                                                                                                                            
                               |     7        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    
           HEM6_LEIMA     - ---MSLAVEAVKDFLLKLQDDICEALEAEDGQATFVEDKWTREGGGGGRTRVMVDGAVIEKGGVNFSHVYGKGLPMSSTERHPDIAGCNFEAMGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRDFHQVAQDLCKPFGADVYARFKGWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYMDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYNWQPEPGTPEARLTEYFLTKRQWV 301
               SCOP domains d1vjub_ B: Hypothetical protein Lmaj006828                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1vjuB00 B:6-309 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) --------Coprogen_oxidas-1vjuB01 B:14-309                                                                                                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) --------Coprogen_oxidas-1vjuB02 B:14-309                                                                                                                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeeeeee....eeeeeeeeeeeeee..---------.....eeeeeeeeeeeee......eeeeeeeeeeee......eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhheehhhhee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh...............hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------COPROGEN_OXIDASE         ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vju B   6 HHHmSLAVEAVKDFLLKLQDDICEALEAEDGQATFVEDKWTREGGGGGRTRVmVDGAVIEKGGVNFSHVYGKGL---------DIAGCNFEAmGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRDFHQVAQDLCKPFGADVYARFKGWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYmDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYNWQPEPGTPEARLTEYFLTKRQWV 309
                               |    15        25        35        45        55  |     65        75   |     -   |    95  |    105       115       125       135       145       155       165       175       185       195       205       215   |   225       235       245       255       265       275       285       295       305    
                               9-MSE                                           58-MSE               79        89       98-MSE                                                                                                                  219-MSE

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Coproporphyrinogen III oxidase (24)

Superfamily: Coproporphyrinogen III oxidase (11)

Family: Coproporphyrinogen III oxidase (10)

Protein domain: Hypothetical protein Lmaj006828 (1)

Leishmania major [TaxId: 5664] (1)

1a	d1vjua_	A:
1b	d1vjub_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: oxygen-dependent coproporphyrinogen oxidase (11)

Homologous Superfamily: oxygen-dependent coproporphyrinogen oxidase (11)

Leishmania major. Organism_taxid: 5664. (1)

1a	1vjuB00	B:6-309
1b	1vjuA00	A:8-309

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Coprogen_oxidas] (5)

Family: Coprogen_oxidas (5)

Leishmania major (2)

1a	Coprogen_oxidas-1vjuB01	B:14-309
1b	Coprogen_oxidas-1vjuB02	B:14-309

Asymmetric Unit(hide GO term definitions)

Chain A,B (HEM6_LEIMA | P84155)

molecular function
	GO:0004109	coproporphyrinogen oxidase activity	Catalysis of the reaction: coproporphyrinogen III + 2 H(+) + O(2) = 2 CO(2) + 2 H(2)O + protoporphyrinogen IX.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
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.

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