3B98 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ZEBRAFISH PROSTACYCLIN SYNTHASE (CYTOCHROME P450 8A1)

Authors :   Y. -C. Li, C. -W. Chiang, H. -C. Yeh, P. -Y. Hsu, F. G. Whitby, L. -H. Wang, N. -L. Chan

Date :   03 Nov 07 (Deposition) - 20 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.08

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

Keywords :   Prostacyclin Synthase, Cytochrome P450 8A1, Cyp8A1, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. -C. Li, C. -W. Chiang, H. -C. Yeh, P. -Y. Hsu, F. G. Whitby, L. -H. Wang, N. -L. Chan
Structures Of Prostacyclin Synthase And Its Complexes With Substrate Analog And Inhibitor Reveal A Ligand-Specific Heme Conformation Change
J. Biol. Chem. V. 283 2917 2008
PubMed-ID: 18032380 | Reference-DOI: 10.1074/JBC.M707470200
(for further references see the PDB file header)

Molecule 1 - PROSTAGLANDIN I2 SYNTHASE
	Chains	:	A, B
	EC Number	:	5.3.99.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 17-480
	Gene	:	PGIS
	Organism Common	:	ZEBRAFISH
	Organism Scientific	:	DANIO RERIO
	Organism Taxid	:	7955
	Synonym	:	CYTOCHROME P450 8A1, PROSTACYCLIN SYNTHASE

		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, 2)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:119 , VAL A:273 , THR A:274 , ASN A:277 , PRO A:413 , TRP A:414 , CYS A:421 , PRO A:422 , GLY A:423 , PHE A:426 , HOH A:642 , HOH A:663 , HOH A:768	BINDING SITE FOR RESIDUE HEM A 600
2	AC2	SOFTWARE	GLN B:94 , VAL B:273 , THR B:274 , ASN B:277 , ALA B:278 , PRO B:413 , TRP B:414 , CYS B:421 , PRO B:422 , GLY B:423 , PHE B:426 , ALA B:427 , ILE B:465	BINDING SITE FOR RESIDUE HEM B 600

(no "SS Bond" information available for 3B98)

Asymmetric Unit

No.	Residues
1	Ser A:370	-	Pro A:371
2	Ser B:370	-	Pro B:371

(no "SAP(SNP)/Variant" information available for 3B98)

(no "PROSITE Motif" information available for 3B98)

Asymmetric Unit (10, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSDART00000084334	1	ENSDARE00000613519	chr6:46526910-46526805	106	PTGIS_DANRE	1-24	24	2	A:22-24 B:22-24	3 3
1.2	ENSDART00000084334	2	ENSDARE00000613638	chr6:46526690-46526567	124	PTGIS_DANRE	24-65	42	2	A:24-65 B:24-65	42 42
1.3	ENSDART00000084334	3	ENSDARE00000613508	chr6:46522867-46522692	176	PTGIS_DANRE	66-124	59	2	A:66-124 B:66-124	59 59
1.4	ENSDART00000084334	4	ENSDARE00000613623	chr6:46522416-46522270	147	PTGIS_DANRE	124-173	50	2	A:124-173 B:124-173 (gaps)	50 50
1.5	ENSDART00000084334	5	ENSDARE00000613615	chr6:46519656-46519532	125	PTGIS_DANRE	173-215	43	2	A:173-215 B:173-215 (gaps)	43 43
1.6	ENSDART00000084334	6	ENSDARE00000613607	chr6:46519418-46519237	182	PTGIS_DANRE	215-275	61	2	A:215-275 B:215-275 (gaps)	61 61
1.7	ENSDART00000084334	7	ENSDARE00000613593	chr6:46513254-46513116	139	PTGIS_DANRE	276-322	47	2	A:276-322 (gaps) B:276-322 (gaps)	47 47
1.8b	ENSDART00000084334	8b	ENSDARE00000613573	chr6:46512280-46512099	182	PTGIS_DANRE	322-382	61	2	A:322-382 B:322-382	61 61
1.9b	ENSDART00000084334	9b	ENSDARE00000613553	chr6:46508242-46508091	152	PTGIS_DANRE	383-433	51	2	A:383-433 B:383-433	51 51
1.10b	ENSDART00000084334	10b	ENSDARE00000613455	chr6:46505617-46505303	315	PTGIS_DANRE	433-480	48	2	A:433-479 B:433-479	47 47

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:446
 aligned with PTGIS_DANRE | F1RE08 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:458
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471        
          PTGIS_DANRE    22 RTRRRNEPPLDKGMIPWLGHALEFGKDAAKFLTRMKEKHGDIFTVRAAGLYITVLLDSNCYDAVLSDVASLDQTSYAQVLMKRIFNMILPSHNPESEKKRAEMHFQGASLTQLSNSMQNNLRLLMTPSEMGLKTSEWKKDGLFNLCYSLLFKTGYLTVFGAENNDSAALTQIYEEFRRFDKLLPKLARTTINKEEKQIASAAREKLWKWLTPSGLDRKPREQSWLGSYVKQLQDEGIDAEMQRRAMLLQLWVTQGNAGPAAFWVMGYLLTHPEALRAVREEIQGGKHLRLEERQKNTPVFDSVLWETLRLTAAALITRDVTQDKKIRLSNGQEYHLRRGDRLCVFPFISPQMDPQIHQQPEMFQFDRFLNADRTEKKDFFKNGARVKYPSVPWGTEDNLCPGRHFAVHAIKELVFTILTRFDVELCDKNATVPLVDPSRYGFGILQPAGDLEIRYRIR 479
               SCOP domains d3b98a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee........hhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee....hhhhhhh....eehhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh------------.hhhhhhhhhhhhhhheee.eeeee...eeee.....eeee....eeee.........................................................hhhhhhhhhhhhhhhhhhheeeee..........hhhhh.eee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1-----------------------------------------Exon 1.3  PDB: A:66-124 UniProt: 66-124                    ------------------------------------------------Exon 1.5  PDB: A:173-215 UniProt: 173-215  ------------------------------------------------------------Exon 1.7  PDB: A:276-322 (gaps)                --------------------------------------------------------------------------------------------------------------Exon 1.10b  PDB: A:433-479 UniProt: 433-480     Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: A:24-65 UniProt: 24-65     ----------------------------------------------------------Exon 1.4  PDB: A:124-173 UniProt: 124-173         -----------------------------------------Exon 1.6  PDB: A:215-275 UniProt: 215-275                    ----------------------------------------------Exon 1.8b  PDB: A:322-382 UniProt: 322-382                   Exon 1.9b  PDB: A:383-433 UniProt: 383-433         ---------------------------------------------- Transcript 1 (2)
                 3b98 A  22 RTRRRNEPPLDKGMIPWLGHALEFGKDAAKFLTRMKEKHGDIFTVRAAGLYITVLLDSNCYDAVLSDVASLDQTSYAQVLMKRIFNMILPSHNPESEKKRAEMHFQGASLTQLSNSMQNNLRLLMTPSEMGLKTSEWKKDGLFNLCYSLLFKTGYLTVFGAENNNSAALTQIYEEFRRFDKLLPKLARTTVNKEEKQIASAAREKLWKWLTPSGLDRKPREQSWLGSYVKQLQDEGIDAEMQRRAMLLQLWVTQGNAGPAAFWVMGYLLTHPEALRAVREEIQ------------NTPVFDSVLWETLRLTAAALITRDVTQDKKICLSNGQEYHLRRGDRLCVFPFISPQMDPQIHQQPEMFQFDRFLNADRTEKKDFFKNGARVKYPSVPWGTEDNLCPGRHFAVHAIKELVFTILTRFDVELCDKNATVPLVDPSRYGFGILQPAGDLEIRYRIR 479
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301  |      -     | 321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471        
                                                                                                                                                                                                                                                                                                                    304          317

Chain B from PDB  Type:PROTEIN  Length:427
 aligned with PTGIS_DANRE | F1RE08 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:458
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471        
          PTGIS_DANRE    22 RTRRRNEPPLDKGMIPWLGHALEFGKDAAKFLTRMKEKHGDIFTVRAAGLYITVLLDSNCYDAVLSDVASLDQTSYAQVLMKRIFNMILPSHNPESEKKRAEMHFQGASLTQLSNSMQNNLRLLMTPSEMGLKTSEWKKDGLFNLCYSLLFKTGYLTVFGAENNDSAALTQIYEEFRRFDKLLPKLARTTINKEEKQIASAAREKLWKWLTPSGLDRKPREQSWLGSYVKQLQDEGIDAEMQRRAMLLQLWVTQGNAGPAAFWVMGYLLTHPEALRAVREEIQGGKHLRLEERQKNTPVFDSVLWETLRLTAAALITRDVTQDKKIRLSNGQEYHLRRGDRLCVFPFISPQMDPQIHQQPEMFQFDRFLNADRTEKKDFFKNGARVKYPSVPWGTEDNLCPGRHFAVHAIKELVFTILTRFDVELCDKNATVPLVDPSRYGFGILQPAGDLEIRYRIR 479
               SCOP domains d3b98b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee........hhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh....eehhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........---.eeeehhhhhhhhhhhhhhhhhh..----hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh------------hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh------------.hhhhhhhhhhhhhhhh...eeeee...eeee.....eeee....eeee...................................ee..ee................hhhhhhhhhhhhhhhhhhheeeee..........hhhhh...........eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1-----------------------------------------Exon 1.3  PDB: B:66-124 UniProt: 66-124                    ------------------------------------------------Exon 1.5  PDB: B:173-215 (gaps)            ------------------------------------------------------------Exon 1.7  PDB: B:276-322 (gaps)                --------------------------------------------------------------------------------------------------------------Exon 1.10b  PDB: B:433-479 UniProt: 433-480     Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: B:24-65 UniProt: 24-65     ----------------------------------------------------------Exon 1.4  PDB: B:124-173 (gaps) UniProt: 124-173  -----------------------------------------Exon 1.6  PDB: B:215-275 (gaps) UniProt: 215-275             ----------------------------------------------Exon 1.8b  PDB: B:322-382 UniProt: 322-382                   Exon 1.9b  PDB: B:383-433 UniProt: 383-433         ---------------------------------------------- Transcript 1 (2)
                 3b98 B  22 RTRRRNEPPLDKGMIPWLGHALEFGKDAAKFLTRMKEKHGDIFTVRAAGLYITVLLDSNCYDAVLSDVASLDQTSYAQVLMKRIFNMILPSHNPESEKKRAEMHFQGASLTQLSNSMQNNLRLLMTPSEMGLK---WKKDGLFNLCYSLLFKTGYLTVFGA----SAALTQIYEEFRRFDKLLPKLARTTVNKEEKQIASAAREKLWKWL------------SWLGSYVKQLQDEGIDAEMQRRAMLLQLWVTQGNAGPAAFWVMGYLLTHPEALRAVREEIQ------------NTPVFDSVLWETLRLTAAALITRDVTQDKKICLSNGQEYHLRRGDRLCVFPFISPQMDPQIHQQPEMFQFDRFLNADRTEKKDFFKNGARVKYPSVPWGTEDNLCPGRHFAVHAIKELVFTILTRFDVELCDKNATVPLVDPSRYGFGILQPAGDLEIRYRIR 479
                                    31        41        51        61        71        81        91       101       111       121       131       141       151  |   |161       171       181|    | 191       201       211       221       231         -  |    251       261       271       281       291       301  |      -     | 321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471        
                                                                                                                                                              154 158                     182  187                                         231          244                                                         304          317

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Cytochrome P450 (480)

Superfamily: Cytochrome P450 (480)

Family: automated matches (157)

Protein domain: automated matches (157)

Zebrafish (Danio rerio) [TaxId: 7955] (2)

1a	d3b98a_	A:
1b	d3b98b_	B:

(no "CATH Domain" information available for 3B98)

(no "Pfam Domain" information available for 3B98)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PTGIS_DANRE | F1RE08)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
	GO:0008116	prostaglandin-I synthase activity	Catalysis of the reaction: prostaglandin H(2) = prostaglandin I(2).
biological process
	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:0001516	prostaglandin biosynthetic process	The chemical reactions and pathways resulting in the formation of prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	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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	Cis Peptide Bonds
		Ser A:370 - Pro A:371	[ RasMol ]
		Ser B:370 - Pro B:371	[ RasMol ]

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	3b98
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	5.3.99.4
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	PTGIS_DANRE \| F1RE08	:	3b99

3b6h	THE LIGAND FORM OF THE SAME PROTEIN FROM HUMAN
3b99	THE LIGAND FORM OF THE SAME PROTEIN

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

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