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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF COPROPORPHYRINOGEN III OXIDASE

Authors :   D. Kumaran, S. Swaminathan, S. K. Burley, New York Sgx Research Cen Structural Genomics (Nysgxrc)

Date :   05 Jul 04 (Deposition) - 30 Nov 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Structural Genomics, Dimer, Novel Fold, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Kumaran, S. Swaminathan
Crystal Structure Of Coproporphyrinogen Iii Oxidase
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 Taxid	:	562
	Gene	:	HEM13, YDR044W, YD5112.02
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	COPROPORPHYRINOGENASE, COPROGEN OXIDASE, COX

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 13)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:188 , PHE A:213 , ASP A:214 , TYR A:216 , HOH A:529 , HOH A:540 , HOH A:566 , HOH A:695	BINDING SITE FOR RESIDUE GOL A 500

Asymmetric/Biological Unit

No.	Residues
1	A:193	-	B:193

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

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

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_YEAST	190-214	2	A:190-214 B:190-214

Asymmetric/Biological Unit (1, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YDR044W	1	YDR044W.1	IV:546641-547627	987	HEM6_YEAST	1-328	328	2	A:2-270 (gaps) B:2-270 (gaps)	269 269

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:259
 aligned with HEM6_YEAST | P11353 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:269
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261         
           HEM6_YEAST     2 PAPQDPRNLPIRQQMEALIRRKQAEITQGLESIDTVKFHADTWTRGNDGGGGTSMVIQDGTTFEKGGVNVSVVYGQLSPAAVSAMKADHKNLRLPEDPKTGLPVTDGVKFFACGLSMVIHPVNPHAPTTHLNYRYFETWNQDGTPQTWWFGGGADLTPSYLYEEDGQLFHQLHKDALDKHDTALYPRFKKWCDEYFYITHRKETRGIGGIFFDDYDERDPQEILKMVEDCFDAFLPSYLTIVKRRKDMPYTKEEQQWQAIRRGRYVEFN 270
               SCOP domains d1txna_ A: Coproporphyrinogen III oxidase                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1txnA00 A:2-270 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhh......ee.............eeeee....eeeeeeeeeeeeeeehhhhhhhhhhhh......----------..eeeeeeeeeeeeee......eeeeeeeeeeee.....eeeeeeeeeeeee....hhhhhhhhhhhhhhhhhh...hhhhhheehhhhhhhhhh.......eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPROGEN_OXIDASE         -------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:2-270 (gaps) UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                     Transcript 1
                 1txn A   2 PAPQDPRNLPIRQQmEALIRRKQAEITQGLESIDTVKFHADTWTRGNDGGGGTSmVIQDGTTFEKGGVNVSVVYGQLSPAAVSAmKADHKNLRLP----------DGVKFFACGLSmVIHPVNPHAPTTHLNYRYFETWNQDGTPQTWWFGGGADLTPSYLYEEDGQLFHQLHKDALDKHDTALYPRFKKWCDEYFYITHRKETRGIGGIFFDDYDERDPQEILKmVEDCFDAFLPSYLTIVKRRKDmPYTKEEQQWQAIRRGRYVEFN 270
                                    11    |   21        31        41        51    |   61        71        81    |   91    |    -     | 111      |121       131       141       151       161       171       181       191       201       211       221     | 231       241       251       261         
                                         16-MSE                                  56-MSE                        86-MSE    96        107        118-MSE                                                                                                      227-MSE               249-MSE

Chain B from PDB  Type:PROTEIN  Length:256
 aligned with HEM6_YEAST | P11353 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:269
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261         
           HEM6_YEAST     2 PAPQDPRNLPIRQQMEALIRRKQAEITQGLESIDTVKFHADTWTRGNDGGGGTSMVIQDGTTFEKGGVNVSVVYGQLSPAAVSAMKADHKNLRLPEDPKTGLPVTDGVKFFACGLSMVIHPVNPHAPTTHLNYRYFETWNQDGTPQTWWFGGGADLTPSYLYEEDGQLFHQLHKDALDKHDTALYPRFKKWCDEYFYITHRKETRGIGGIFFDDYDERDPQEILKMVEDCFDAFLPSYLTIVKRRKDMPYTKEEQQWQAIRRGRYVEFN 270
               SCOP domains d1txnb_ B: Coproporphyrinogen III oxidase                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1txnB00 B:2-270 oxygen-dependent coproporphyrinogen oxidase                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) ------------Coprogen_oxidas-1txnB01 B:14-270                                                                                                                                                                                                                                  Pfam domains (1)
           Pfam domains (2) ------------Coprogen_oxidas-1txnB02 B:14-270                                                                                                                                                                                                                                  Pfam domains (2)
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhh......ee.............eeeee....eeeeeeeeeeeeeeehhhhhhhhhhhh......----------..eeeeeeeeeeeeee......eeeeeeeeeeee.....eeeeeeeeeeeee....hhhhhhhhhhhhhhhhhh...hhhhhhh.hhhhhhhhhh.---...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COPROGEN_OXIDASE         -------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-270 (gaps) UniProt: 1-328 [INCOMPLETE]                                                                                                                                                                                                                     Transcript 1
                 1txn B   2 PAPQDPRNLPIRQQmEALIRRKQAEITQGLESIDTVKFHADTWTRGNDGGGGTSmVIQDGTTFEKGGVNVSVVYGQLSPAAVSAmKADHKNLRLP----------DGVKFFACGLSmVIHPVNPHAPTTHLNYRYFETWNQDGTPQTWWFGGGADLTPSYLYEEDGQLFHQLHKDALDKHDTALYPRFKKWCDEYFYITHR---RGIGGIFFDDYDERDPQEILKmVEDCFDAFLPSYLTIVKRRKDmPYTKEEQQWQAIRRGRYVEFN 270
                                    11    |   21        31        41        51    |   61        71        81    |   91    |    -     | 111      |121       131       141       151       161       171       181       191       201|   |  211       221     | 231       241       251       261         
                                         16-MSE                                  56-MSE                        86-MSE    96        107        118-MSE                                                                             202 206                  227-MSE               249-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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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: Coproporphyrinogen III oxidase (4)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (4)

1a	d1txna_	A:
1b	d1txnb_	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)

Baker's yeast (Saccharomyces cerevisiae) (4)

1a	1txnA00	A:2-270
1b	1txnB00	B:2-270

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Coprogen_oxidas (5)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (3)

1a	Coprogen_oxidas-1txnB01	B:14-270
1b	Coprogen_oxidas-1txnB02	B:14-270

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HEM6_YEAST | P11353)

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.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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SS Bonds (1, 1)

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