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Asym./Biol. Unit (Jmol Viewer)

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Title :   LEISHMANIA MAJOR COPROPORPHYRINOGEN III OXIDASE WITH BOUND LIGAND

Authors :   I. Le Trong, E. A. Merritt, Structural Genomics Of Pathogenic Pro Consortium (Sgpp)

Date :   22 Jul 08 (Deposition) - 09 Sep 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.66

Chains :   Asym./Biol. Unit : A,B

Keywords :   Fragment Cocktail, Structural Genomics, Structural Genomics Of Pathogenic Protozoa Consortium, Sgpp, Heme Biosynthesis, Oxidoreductase, Porphyrin Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. A. Merritt, I. Le Trong, E. T. Larson, S. Shibata, Z. Zhang, L. Anderson, J. Ross, C. L. M. J. Verlinde, F. S. Buckner, W. C. Van Voorhis, G. J. W. Hol, E. Fan
Leishmania Major Coproporphyrinogen Iii Oxidase With Bound Ligand
To Be Published
PubMed: search

Molecule 1 - COPROPORPHYRINOGEN III OXIDASE
	Chains	:	A, B
	EC Number	:	1.3.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET14B, BG1861
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LMAJ006828, LMJF06.1270
	Organism Scientific	:	LEISHMANIA MAJOR
	Organism Taxid	:	5664
	Strain	:	FRIEDLIN
	Synonym	:	COPROPORPHYRINOGENASE, COPROGEN OXIDASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 11)

No.	Name	Count	Type	Full Name
1	0PA	6	Ligand/Ion	CYCLOPENTYLACETIC ACID
2	ACT	5	Ligand/Ion	ACETATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:107 , ARG A:181 , TYR A:241 , ASN A:245 , HOH A:631	BINDING SITE FOR RESIDUE ACT A 402
02	AC2	SOFTWARE	PRO A:225 , TYR A:226 , HOH A:627	BINDING SITE FOR RESIDUE ACT A 403
03	AC3	SOFTWARE	GLY A:44 , GLY A:45 , PHE A:63 , TYR A:293	BINDING SITE FOR RESIDUE ACT A 404
04	AC4	SOFTWARE	PHE A:32	BINDING SITE FOR RESIDUE ACT A 405
05	AC5	SOFTWARE	HIS B:107 , ARG B:181 , TYR B:241 , ASN B:245 , HOH B:593	BINDING SITE FOR RESIDUE ACT B 401
06	AC6	SOFTWARE	TRP A:37 , ARG A:39 , ASN A:62 , SER A:64 , GLY A:260 , ARG A:261 , HOH A:650	BINDING SITE FOR RESIDUE 0PA A 501
07	AC7	SOFTWARE	SER A:93 , GLY A:251 , THR A:252 , SER A:264 , ILE A:265 , ILE A:267 , SER A:268 , HOH A:624	BINDING SITE FOR RESIDUE 0PA A 502
08	AC8	SOFTWARE	SER A:64 , MET A:90 , GLY A:91 , SER A:93 , ASN A:109 , HOH A:628 , HOH A:657	BINDING SITE FOR RESIDUE 0PA A 503
09	AC9	SOFTWARE	SER B:64 , SER B:258 , ILE B:265	BINDING SITE FOR RESIDUE 0PA B 504
10	BC1	SOFTWARE	ASN B:62 , SER B:93 , GLY B:251 , SER B:264 , ILE B:265 , ILE B:267 , HOH B:524	BINDING SITE FOR RESIDUE 0PA B 505
11	BC2	SOFTWARE	SER B:64 , MET B:90 , SER B:93 , ASN B:109 , HOH B:581	BINDING SITE FOR RESIDUE 0PA B 506

(no "SS Bond" information available for 3DWR)

(no "Cis Peptide Bond" information available for 3DWR)

(no "SAP(SNP)/Variant" information available for 3DWR)

Asymmetric/Biological 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:165-189 B:165-189

(no "Exon" information available for 3DWR)

Asymmetric/Biological 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:286
 aligned with HEM6_LEIMA | P84155 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:301
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
           HEM6_LEIMA     1 MSLAVEAVKDFLLKLQDDICEALEAEDGQATFVEDKWTREGGGGGRTRVMVDGAVIEKGGVNFSHVYGKGLPMSSTERHPDIAGCNFEAMGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRDFHQVAQDLCKPFGADVYARFKGWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYMDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYNWQPEPGTPEARLTEYFLTKRQWV 301
               SCOP domains d3dwra_ A: automated matches                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3dwrA00 A:1-301 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee....eeeeeeeeeeee.---------------...eeeeeeeeeeee......eeeeeeeeeeeee..eeeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhheehhhhee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..eee..........hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------COPROGEN_OXIDASE         ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwr A   1 MSLAVEAVKDFLLKLQDDICEALEAEDGQATFVEDKWTREGGGGGRTRVMVDGAVIEKGGVNFSHVYG---------------GCNFEAMGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRDFHQVAQDLCKPFGADVYARFKGWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYMDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYNWQPEPGTPEARLTEYFLTKRQWV 301
                                    10        20        30        40        50        60       | -         -   |    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
                                                                                              68              84

Chain B from PDB  Type:PROTEIN  Length:275
 aligned with HEM6_LEIMA | P84155 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:301
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
           HEM6_LEIMA     1 MSLAVEAVKDFLLKLQDDICEALEAEDGQATFVEDKWTREGGGGGRTRVMVDGAVIEKGGVNFSHVYGKGLPMSSTERHPDIAGCNFEAMGVSLVIHPKNPHVPTSHANVRLFVAEREGKEPVWWFGGGFDLTPYYAVEEDCRDFHQVAQDLCKPFGADVYARFKGWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYMDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYNWQPEPGTPEARLTEYFLTKRQWV 301
               SCOP domains d3dwrb_ B: automated matches                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3dwrB00 B:1-301 oxygen-dependent copro     porphyrinogen oxidase                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.-----.eeeeeee....eeeeeeeeeee.----------------...eeeeeeeeeeee......eeeeeeeeeee.-----.eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhheehhhhee...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..eee..........hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------COPROGEN_OXIDASE         ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwr B   1 MSLAVEAVKDFLLKLQDDICEALEAEDGQATFVEDKWT-----GGRTRVMVDGAVIEKGGVNFSHVY----------------GCNFEAMGVSLVIHPKNPHVPTSHANVRLFVAE-----PVWWFGGGFDLTPYYAVEEDCRDFHQVAQDLCKPFGADVYARFKGWCDEYFFIPYRNEARGIGGLFFDDLNEWPFEKCFEFVQAVGKGYMDAYIPIVNRRKNTPYTEQQVEFQEFRRGRYAEFNLVIDRGTKFGLQSGGRTESILISLPPRARWGYNWQPEPGTPEARLTEYFLTKRQWV 301
                                    10        20        30       | -   |    50        60      |  -         -   |    90       100       110     |   - |     130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300 
                                                                38    44                     67               84                             116   122

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/Biological Unit

Classes(

)

Folds(

)

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: automated matches (5)

Leishmania major [TaxId: 5664] (3)

1a	d3dwra_	A:
1b	d3dwrb_	B:

Asymmetric/Biological 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. Strain: friedlin. (2)

1a	3dwrA00	A:1-301
1b	3dwrB00	B:1-301

(no "Pfam Domain" information available for 3DWR)

Asymmetric/Biological 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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	HEM6_LEIMA \| P84155	:	1vju 2qt8 3dws

Description

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Ligands, Modified Residues, Ions (2, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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