1B6Z - JenaLib

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Title :   6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE

Authors :   T. Ploom, B. Thoeny, J. Yim, S. Lee, H. Nar, W. Leimbacher, R. Huber, J. Ri G. Auerbach

Date :   18 Jan 99 (Deposition) - 21 Jan 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (3x)

Keywords :   Pterin, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Ploom, B. Thony, J. Yim, S. Lee, H. Nar, W. Leimbacher, J. Richardson R. Huber, G. Auerbach
Crystallographic And Kinetic Investigations On The Mechanis Of 6-Pyruvoyl Tetrahydropterin Synthase.
J. Mol. Biol. V. 286 851 1999
PubMed-ID: 10024455 | Reference-DOI: 10.1006/JMBI.1998.2511

Molecule 1 - 6-PYRUVOYL TETRAHYDROPTERIN SYNTHASE
	Chains	:	A, B
	EC Number	:	4.6.1.10
	Fragment	:	PTERIN BINDING DOMAIN
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	PTPS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:23 , HIS A:48 , HIS A:50 , GLU A:133 , HOH A:469	BINDING SITE FOR RESIDUE ZN A 401
2	AC2	SOFTWARE	HIS B:23 , HIS B:48 , HIS B:50 , GLU B:133 , HOH B:457	BINDING SITE FOR RESIDUE ZN B 402

(no "SS Bond" information available for 1B6Z)

(no "Cis Peptide Bond" information available for 1B6Z)

(no "SAP(SNP)/Variant" information available for 1B6Z)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PTPS_1	PS00987	6-pyruvoyl tetrahydropterin synthase signature 1.	PTPS_RAT	42-52	2	A:42-52 B:42-52
2	PTPS_2	PS00988	6-pyruvoyl tetrahydropterin synthase signature 2.	PTPS_RAT	88-95	2	A:88-95 B:88-95

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PTPS_1	PS00987	6-pyruvoyl tetrahydropterin synthase signature 1.	PTPS_RAT	42-52	2	A:42-52 B:42-52
2	PTPS_2	PS00988	6-pyruvoyl tetrahydropterin synthase signature 2.	PTPS_RAT	88-95	2	A:88-95 B:88-95

Biological Unit 2 (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PTPS_1	PS00987	6-pyruvoyl tetrahydropterin synthase signature 1.	PTPS_RAT	42-52	6	A:42-52 B:42-52
2	PTPS_2	PS00988	6-pyruvoyl tetrahydropterin synthase signature 2.	PTPS_RAT	88-95	6	A:88-95 B:88-95

Asymmetric Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000012434	1	ENSRNOE00000086947	chr8:53887711-53887582	130	PTPS_RAT	1-27	27	2	A:7-27 B:7-27	21 21
1.2	ENSRNOT00000012434	2	ENSRNOE00000087175	chr8:53885920-53885841	80	PTPS_RAT	27-54	28	2	A:27-54 B:27-54	28 28
1.3	ENSRNOT00000012434	3	ENSRNOE00000087366	chr8:53884570-53884548	23	PTPS_RAT	54-61	8	2	A:54-61 B:54-61	8 8
1.4	ENSRNOT00000012434	4	ENSRNOE00000087547	chr8:53884073-53884017	57	PTPS_RAT	62-80	19	2	A:62-80 B:62-80	19 19
1.5	ENSRNOT00000012434	5	ENSRNOE00000087723	chr8:53881773-53881703	71	PTPS_RAT	81-104	24	2	A:81-104 B:81-104	24 24
1.6	ENSRNOT00000012434	6	ENSRNOE00000087895	chr8:53881516-53880701	816	PTPS_RAT	104-144	41	2	A:104-144 B:104-144	41 41

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:138
 aligned with PTPS_RAT | P27213 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:138
                                    16        26        36        46        56        66        76        86        96       106       116       126       136        
             PTPS_RAT     7 LRRRARLSRLVSFSASHRLHSPSLSAEENLKVFGKCNNPNGHGHNYKVVVTIHGEIDPVTGMVMNLTDLKEYMEEAIMKPLDHKNLDLDVPYFADVVSTTENVAVYIWENLQRLLPVGALYKVKVYETDNNIVVYKGE 144
               SCOP domains d1b6za_ A: 6-pyruvoyl tetrahydropterin synthase                                                                                            SCOP domains
               CATH domains 1b6zA00 A:7-144  [code=3.30.479.10, no name defined]                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeee........hhhhhhhhhhhh....eeeeeeeeeeeeee..........hhhhhhhhhhh.hhhh....hhhh.hhhh.....hhhhhhhhhhhhhhh.....eeeeeeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------PTPS_1     -----------------------------------PTPS_2  ------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:7-27--------------------------Exon 1.3Exon 1.4           Exon 1.5  PDB: A:81-104 ---------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.2  PDB: A:27-54      -------------------------------------------------Exon 1.6  PDB: A:104-144 UniProt: 104-144 Transcript 1 (2)
                 1b6z A   7 LRRRARLSRLVSFSASHRLHSPSLSAEENLKVFGKCNNPNGHGHNYKVVVTIHGEIDPVTGMVMNLTDLKEYMEEAIMKPLDHKNLDLDVPYFADVVSTTENVAVYIWENLQRLLPVGALYKVKVYETDNNIVVYKGE 144
                                    16        26        36        46        56        66        76        86        96       106       116       126       136

Chain B from PDB  Type:PROTEIN  Length:138
 aligned with PTPS_RAT | P27213 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:138
                                    16        26        36        46        56        66        76        86        96       106       116       126       136        
             PTPS_RAT     7 LRRRARLSRLVSFSASHRLHSPSLSAEENLKVFGKCNNPNGHGHNYKVVVTIHGEIDPVTGMVMNLTDLKEYMEEAIMKPLDHKNLDLDVPYFADVVSTTENVAVYIWENLQRLLPVGALYKVKVYETDNNIVVYKGE 144
               SCOP domains d1b6zb_ B: 6-pyruvoyl tetrahydropterin synthase                                                                                            SCOP domains
               CATH domains 1b6zB00 B:7-144  [code=3.30.479.10, no name defined]                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeee........hhhhhhhhhhhh....eeeeeeeeeeeeee..........hhhhhhhhhhh.hhhh....hhhh.hhhh.....hhhhhhhhhhhhhhh.....eeeeeee.....eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------PTPS_1     -----------------------------------PTPS_2  ------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:7-27--------------------------Exon 1.3Exon 1.4           Exon 1.5  PDB: B:81-104 ---------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.2  PDB: B:27-54      -------------------------------------------------Exon 1.6  PDB: B:104-144 UniProt: 104-144 Transcript 1 (2)
                 1b6z B   7 LRRRARLSRLVSFSASHRLHSPSLSAEENLKVFGKCNNPNGHGHNYKVVVTIHGEIDPVTGMVMNLTDLKEYMEEAIMKPLDHKNLDLDVPYFADVVSTTENVAVYIWENLQRLLPVGALYKVKVYETDNNIVVYKGE 144
                                    16        26        36        46        56        66        76        86        96       106       116       126       136

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)

Norway rat (Rattus norvegicus) [TaxId: 10116] (3)

1a	d1b6za_	A:
1b	d1b6zb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

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)

Norway rat (Rattus norvegicus) (1)

1a	1b6zA00	A:7-144
1b	1b6zB00	B:7-144

(no "Pfam Domain" information available for 1B6Z)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PTPS_RAT | P27213)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
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.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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Description

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