1VBJ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF PROSTAGLANDIN F SYNTHASE FROM TRYPANOSOMA BRUCEI

Authors :   T. Inoue

Date :   27 Feb 04 (Deposition) - 12 Apr 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Tim Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Inoue
The Crystal Structure Of Prostaglandin F Synthase From Trypanosoma Brucei
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROSTAGLANDIN F SYNTHASE
	Chains	:	A, B
	EC Number	:	1.1.1.188
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGX4T-1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	TRYPANOSOMA BRUCEI
	Organism Taxid	:	5691

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	CIT	2	Ligand/Ion	CITRIC ACID
2	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:21 , MET A:22 , TRP A:23 , ASP A:47 , TYR A:52 , LYS A:77 , HIS A:110 , SER A:139 , ASN A:140 , GLN A:161 , TRP A:187 , SER A:188 , PRO A:189 , LEU A:190 , GLY A:191 , GLN A:192 , GLY A:193 , VAL A:196 , ALA A:213 , ILE A:228 , PRO A:229 , LYS A:230 , SER A:231 , GLY A:232 , ARG A:236 , GLU A:239 , ASN A:240 , CIT A:4001 , HOH A:4024 , HOH A:4026 , HOH A:4082 , HOH A:4126	BINDING SITE FOR RESIDUE NAP A 3001
2	AC2	SOFTWARE	GLY B:21 , MET B:22 , TRP B:23 , ASP B:47 , TYR B:52 , LYS B:77 , HIS B:110 , SER B:139 , ASN B:140 , GLN B:161 , TRP B:187 , SER B:188 , PRO B:189 , LEU B:190 , GLY B:191 , GLN B:192 , GLY B:193 , VAL B:196 , ALA B:213 , ILE B:228 , PRO B:229 , LYS B:230 , SER B:231 , GLY B:232 , ARG B:236 , GLU B:239 , ASN B:240 , CIT B:4002 , HOH B:4074 , HOH B:4128	BINDING SITE FOR RESIDUE NAP B 3002
3	AC3	SOFTWARE	TRP A:23 , ILE A:51 , TYR A:52 , TRP A:79 , HIS A:110 , TRP A:111 , LYS A:131 , NAP A:3001 , HOH A:4249	BINDING SITE FOR RESIDUE CIT A 4001
4	AC4	SOFTWARE	TRP B:23 , TYR B:52 , TRP B:79 , HIS B:110 , TRP B:111 , TRP B:187 , GLY B:266 , PRO B:267 , PHE B:272 , NAP B:3002 , HOH B:4153	BINDING SITE FOR RESIDUE CIT B 4002

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

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	PGFS_TRYBB	42-59	2	A:42-59 B:42-59
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	PGFS_TRYBB	124-141	2	A:124-141 B:124-141

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	PGFS_TRYBB	42-59	1	A:42-59 -
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	PGFS_TRYBB	124-141	1	A:124-141 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	PGFS_TRYBB	42-59	1	- B:42-59
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	PGFS_TRYBB	124-141	1	- B:124-141

(no "Exon" information available for 1VBJ)

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:281
 aligned with PGFS_TRYBB | Q9GV41 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:281
                                 1                                                                                                                                                                                                                                                                                   
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275 
           PGFS_TRYBB     - -----MALTQSLKLSNGVMMPVLGFGMWKLQDGNEAETATMWAIKSGYRHIDTAAIYKNEESAGRAIASCGVPREELFVTTKLWNSDQGYESTLSAFEKSIKKLGLEYVDLYLIHWPGKDKFIDTWKAFEKLYADKKVRAIGVSNFHEHHIEELLKHCKVAPMVNQIELHPLLNQKALCEYCKSKNIAVTAWSPLGQGHLVEDARLKAIGGKYGKTAAQVMLRWEIQAGVITIPKSGNEARIKENGNIFDFELTAEDIQVIDGMNAGHRYGPDPEVFMNDF 276
               SCOP domains d1vbja_ A: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1vbjA00 A:-4-276 NADP-dependent oxidoreductase                                                                                                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.....eee...ee......hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhh..hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh.....eeee......hhhhhhhhhhhhhhh.....eeee..hhhhhhhhhh.......eeeee......hhhhhhhhhhh..eeeee..hhhhh...hhhhhhhhhh...hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------ALDOKETO_REDUCTASE--------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vbj A  -4 GSPEFMALTQSLKLSNGVMMPVLGFGMWKLQDGNEAETATMWAIKSGYRHIDTAAIYKNEESAGRAIASCGVPREELFVTTKLWNSDQGYESTLSAFEKSIKKLGLEYVDLYLIHWPGKDKFIDTWKAFEKLYADKKVRAIGVSNFHEHHIEELLKHCKVAPMVNQIELHPLLNQKALCEYCKSKNIAVTAWSPLGQGHLVEDARLKAIGGKYGKTAAQVMLRWEIQAGVITIPKSGNEARIKENGNIFDFELTAEDIQVIDGMNAGHRYGPDPEVFMNDF 276
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275

Chain B from PDB  Type:PROTEIN  Length:279
 aligned with PGFS_TRYBB | Q9GV41 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:279
                               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         
           PGFS_TRYBB     - ---MALTQSLKLSNGVMMPVLGFGMWKLQDGNEAETATMWAIKSGYRHIDTAAIYKNEESAGRAIASCGVPREELFVTTKLWNSDQGYESTLSAFEKSIKKLGLEYVDLYLIHWPGKDKFIDTWKAFEKLYADKKVRAIGVSNFHEHHIEELLKHCKVAPMVNQIELHPLLNQKALCEYCKSKNIAVTAWSPLGQGHLVEDARLKAIGGKYGKTAAQVMLRWEIQAGVITIPKSGNEARIKENGNIFDFELTAEDIQVIDGMNAGHRYGPDPEVFMNDF 276
               SCOP domains d1vbjb_ B: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1vbjB00 B:-2-276 NADP-dependent oxidoreductase                                                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.....eee...ee......hhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhh..hhhhheeeeeehhhhhhhhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhh......eeeee......hhhhhhhhhhh..eeeee..hhhhh...hhhhhhhhhh...hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------ALDOKETO_REDUCTASE--------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vbj B  -2 PEFMALTQSLKLSNGVMMPVLGFGMWKLQDGNEAETATMWAIKSGYRHIDTAAIYKNEESAGRAIASCGVPREELFVTTKLWNSDQGYESTLSAFEKSIKKLGLEYVDLYLIHWPGKDKFIDTWKAFEKLYADKKVRAIGVSNFHEHHIEELLKHCKVAPMVNQIELHPLLNQKALCEYCKSKNIAVTAWSPLGQGHLVEDARLKAIGGKYGKTAAQVMLRWEIQAGVITIPKSGNEARIKENGNIFDFELTAEDIQVIDGMNAGHRYGPDPEVFMNDF 276
                                     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

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: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: NAD(P)-linked oxidoreductase (286)

Family: automated matches (35)

Protein domain: automated matches (35)

Trypanosome (Trypanosoma brucei) [TaxId: 5691] (1)

1a	d1vbja_	A:
1b	d1vbjb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: NADP-dependent oxidoreductase (181)

Trypanosoma brucei. Organism_taxid: 5691. (1)

1a	1vbjA00	A:-4-276
1b	1vbjB00	B:-2-276

(no "Pfam Domain" information available for 1VBJ)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PGFS_TRYBB | Q9GV41)

molecular function
	GO:0045290	D-arabinose 1-dehydrogenase [NAD(P)+] activity	Catalysis of the reaction: D-arabinose + NAD(P)+ = D-arabinono-1,4-lactone + NAD(P)H + H+.
	GO:0004033	aldo-keto reductase (NADP) activity	Catalysis of the reaction: an alcohol + NADP+ = an aldehyde or a ketone + NADPH + H+.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0036131	prostaglandin D2 11-ketoreductase activity	Catalysis of the reaction: prostaglandin D2 + H+ + NADPH -> 11-epi-prostaglandin F2alpha + NADP+.
	GO:0047017	prostaglandin-F synthase activity	Catalysis of the reaction: NADP+ + (5Z,13E)-(15S)-9-alpha,11-alpha,15-trihydroxyprosta-5,13-dienoate = NADPH + H+ + (5Z,13E)-(15S)-9-alpha,15-dihydroxy-11-oxoprosta-5,13-dienoate.
biological process
	GO:0019571	D-arabinose catabolic process	The chemical reactions and pathways resulting in the breakdown of D-arabinose, the D-enantiomer of arabino-pentose.
	GO:0006633	fatty acid biosynthetic process	The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
	GO:0006631	fatty acid metabolic process	The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	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:0006693	prostaglandin metabolic process	The chemical reactions and pathways involving prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring due to the formation of a bond between two carbons of a fatty acid. They have a wide range of biological activities.
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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1mz7	THE SAME PROTEIN COMPLEXED WITH SULFATE

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Ligands, Modified Residues, Ions (2, 4)

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