1Y13 - JenaLib

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Title :   STRUCTURAL ANALYSIS OF PLASMODIUM FALCIPARUM 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE (PTPS)

Authors :   J. Bosch, W. G. J. Hol, Structural Genomics Of Pathogenic Protozoa Consortium (Sgpp)

Date :   17 Nov 04 (Deposition) - 04 Jan 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

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

Reference :   J. Bosch, W. G. J. Hol, Structural Genomics Of Pathogenic Protozoa Consortium (Sgpp
Structural Analysis Of Plasmodium Falciparum 6-Pyruvoyl Tetrahydropterin Synthase (Ptps)
To Be Published
PubMed: search

Molecule 1 - 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
	Chains	:	A, B, C
	EC Number	:	4.2.3.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET14B
	Expression System Strain	:	BL21STAR(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	MALARIA PARASITE P. FALCIPARUM
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	5833
	Synonym	:	PTPS

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:	A	B	C
Biological Unit 2 (1x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	BIO	3	Ligand/Ion	BIOPTERIN
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	3	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	BIO	6	Ligand/Ion	BIOPTERIN
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	BIO	3	Ligand/Ion	BIOPTERIN
2	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:29 , HIS A:41 , HIS A:43 , BIO A:175	BINDING SITE FOR RESIDUE ZN A 174
2	AC2	SOFTWARE	HIS B:29 , HIS B:41 , HIS B:43 , GLU B:161 , BIO B:175	BINDING SITE FOR RESIDUE ZN B 174
3	AC3	SOFTWARE	HIS C:29 , HIS C:41 , HIS C:43 , GLU C:161 , BIO C:175	BINDING SITE FOR RESIDUE ZN C 174
4	AC4	SOFTWARE	HIS A:29 , ILE A:31 , GLU A:38 , HIS A:41 , HIS A:43 , GLU A:128 , GLU A:161 , ZN A:174 , HIS B:80 , TYR C:60 , ILE C:62 , ASP C:63 , PHE C:64	BINDING SITE FOR RESIDUE BIO A 175
5	AC5	SOFTWARE	TYR A:60 , ILE A:62 , ASP A:63 , PHE A:64 , HIS A:80 , HIS B:29 , ILE B:31 , GLU B:38 , HIS B:41 , HIS B:43 , SER B:126 , THR B:127 , GLU B:128 , GLU B:161 , ZN B:174	BINDING SITE FOR RESIDUE BIO B 175
6	AC6	SOFTWARE	TYR B:60 , ILE B:62 , ASP B:63 , PHE B:64 , ILE C:31 , GLU C:38 , HIS C:41 , HIS C:43 , HIS C:80 , SER C:126 , THR C:127 , GLU C:128 , GLU C:161 , ZN C:174	BINDING SITE FOR RESIDUE BIO C 175

(no "SS Bond" information available for 1Y13)

(no "Cis Peptide Bond" information available for 1Y13)

(no "SAP(SNP)/Variant" information available for 1Y13)

(no "PROSITE Motif" information available for 1Y13)

(no "Exon" information available for 1Y13)

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:163
 aligned with C6KTB6_PLAF7 | C6KTB6 from UniProtKB/TrEMBL  Length:173

    Alignment length:163
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   
         C6KTB6_PLAF7    11 NSSAEVSVESPSFSFNCAHFIAYNGFRETLHGHNYNVSLKVRGYVRDDGYVIDFSILKEKVKKVCNKLDHHFILPIYSDVLKFENVKNNIKIICEDNSEYSFPERDCIKLPIKHSSTEEIGQYILNQLIEEMDVSLLKSRHIHYIEISVSESPTQKAIVHKYI 173
               SCOP domains d1y13a_ A: 6-pyruvoyl tetrahydropterin synthase                                                                                                                     SCOP domains
               CATH domains 1y13A00 A:11-173  [code=3.30.479.10, no name defined]                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeeee..ee..ee...eeeeeeeeeeeee.........hhhhhhhhhhhhhhhhh..eeee.....eeeeee..eeeeee....eeeee...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y13 A  11 NSSAEVSVESPSFSFNCAHFIAYNGFRETLHGHNYNVSLKVRGYVRDDGYVIDFSILKEKVKKVCNKLDHHFILPIYSDVLKFENVKNNIKIICEDNSEYSFPERDCIKLPIKHSSTEEIGQYILNQLIEEmDVSLLKSRHIHYIEISVSESPTQKAIVHKYI 173
                                    20        30        40        50        60        70        80        90       100       110       120       130       140 |     150       160       170   
                                                                                                                                                             142-MSE

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with C6KTB6_PLAF7 | C6KTB6 from UniProtKB/TrEMBL  Length:173

    Alignment length:163
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   
         C6KTB6_PLAF7    11 NSSAEVSVESPSFSFNCAHFIAYNGFRETLHGHNYNVSLKVRGYVRDDGYVIDFSILKEKVKKVCNKLDHHFILPIYSDVLKFENVKNNIKIICEDNSEYSFPERDCIKLPIKHSSTEEIGQYILNQLIEEMDVSLLKSRHIHYIEISVSESPTQKAIVHKYI 173
               SCOP domains d1y13b_ B: 6-pyruvoyl tetrahydropterin synthase                                                                                                                     SCOP domains
               CATH domains 1y13B00 B:11-173  [code=3.30.479.10, no name defined]                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeeee..ee..ee...eeeeeeeeeeeee.........hhhhhhhhhhhhhhhhh..eeee.....eeeeee..eeeeee....eeeee...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y13 B  11 NSSAEVSVESPSFSFNCAHFIAYNGFRETLHGHNYNVSLKVRGYVRDDGYVIDFSILKEKVKKVCNKLDHHFILPIYSDVLKFENVKNNIKIICEDNSEYSFPERDCIKLPIKHSSTEEIGQYILNQLIEEmDVSLLKSRHIHYIEISVSESPTQKAIVHKYI 173
                                    20        30        40        50        60        70        80        90       100       110       120       130       140 |     150       160       170   
                                                                                                                                                             142-MSE

Chain C from PDB  Type:PROTEIN  Length:163
 aligned with C6KTB6_PLAF7 | C6KTB6 from UniProtKB/TrEMBL  Length:173

    Alignment length:163
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170   
         C6KTB6_PLAF7    11 NSSAEVSVESPSFSFNCAHFIAYNGFRETLHGHNYNVSLKVRGYVRDDGYVIDFSILKEKVKKVCNKLDHHFILPIYSDVLKFENVKNNIKIICEDNSEYSFPERDCIKLPIKHSSTEEIGQYILNQLIEEMDVSLLKSRHIHYIEISVSESPTQKAIVHKYI 173
               SCOP domains d1y13c_ C: 6-pyruvoyl tetrahydropterin synthase                                                                                                                     SCOP domains
               CATH domains 1y13C00 C:11-173  [code=3.30.479.10, no name defined]                                                                                                               CATH domains
           Pfam domains (1) -------PTPS-1y13C01 C:18-171                                                                                                                                     -- Pfam domains (1)
           Pfam domains (2) -------PTPS-1y13C02 C:18-171                                                                                                                                     -- Pfam domains (2)
           Pfam domains (3) -------PTPS-1y13C03 C:18-171                                                                                                                                     -- Pfam domains (3)
         Sec.struct. author ...eeeeeeeeeeeeeeee..ee..ee...eeeeeeeeeeeee.........hhhhhhhhhhhhhhhhh..eeee.....eeeeee..eeeeee....eeeee...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y13 C  11 NSSAEVSVESPSFSFNCAHFIAYNGFRETLHGHNYNVSLKVRGYVRDDGYVIDFSILKEKVKKVCNKLDHHFILPIYSDVLKFENVKNNIKIICEDNSEYSFPERDCIKLPIKHSSTEEIGQYILNQLIEEmDVSLLKSRHIHYIEISVSESPTQKAIVHKYI 173
                                    20        30        40        50        60        70        80        90       100       110       120       130       140 |     150       160       170   
                                                                                                                                                             142-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( (-)

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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: T-fold (116)

Superfamily: Tetrahydrobiopterin biosynthesis enzymes-like (113)

Family: 6-pyruvoyl tetrahydropterin synthase (9)

Protein domain: 6-pyruvoyl tetrahydropterin synthase (6)

Malaria parasite (Plasmodium falciparum) [TaxId: 5833] (1)

1a	d1y13a_	A:
1b	d1y13b_	B:
1c	d1y13c_	C:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Tetrahydropterin Synthase; Chain A (11)

Homologous Superfamily: [code=3.30.479.10, no name defined] (8)

Malaria parasite p (Plasmodium falciparum) (1)

1a	1y13A00	A:11-173
1b	1y13B00	B:11-173
1c	1y13C00	C:11-173

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

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Clan: THBO-biosyn (64)

Family: PTPS (5)

Plasmodium falciparum (isolate 3D7) (1)

1a	PTPS-1y13C01	C:18-171
1b	PTPS-1y13C02	C:18-171
1c	PTPS-1y13C03	C:18-171

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (C6KTB6_PLAF7 | C6KTB6)

molecular function
	GO:0003874	6-pyruvoyltetrahydropterin synthase activity	Catalysis of the reaction: 7,8-dihydroneopterin 3'-triphosphate = 6-pyruvoyl-5,6,7,8-tetrahydropterin + H(+) + triphosphate.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006729	tetrahydrobiopterin biosynthetic process	The chemical reactions and pathways resulting in the formation of tetrahydrobiopterin, the reduced form of biopterin (2-amino-4-hydroxy-6-(1,2-dihydroxypropyl)-pteridine). It functions as a hydroxylation coenzyme, e.g. in the conversion of phenylalanine to tyrosine.

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Description

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Ligands, Modified Residues, Ions (3, 9)

Sites (6, 6)

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