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Title :   CRYSTAL STRUCTURE OF A 6-PYRUVOYLTETRAHYDROPTERIN SYNTHASE HOMOLOGUE FROM ESHERICHIA COLI COMPLEXED SEPIAPTERIN

Authors :   K. H. Seo, N. N. Zhuang, K. H. Lee

Date :   08 Feb 11 (Deposition) - 07 Dec 11 (Release) - 28 May 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   6-Pyruvoyltetrahydropterin Synthase, Bh4 Synthase, Zn, Sepaitperin, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. H. Seo, N. Zhuang, Y. S. Park, K. H. Park, K. H. Lee
Structural Basis Of A Novel Activity Of Bacterial 6-Pyruvoyltetrahydropterin Synthase Homologues Distinct Fro Mammalian 6-Pyruvoyltetrahydropterin Synthase Activity.
Acta Crystallogr. , Sect. D V. 70 1212 2014
PubMed-ID: 24816091 | Reference-DOI: 10.1107/S1399004714002016

Molecule 1 - 6-CARBOXY-5,6,7,8-TETRAHYDROPTERIN SYNTHASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	4.1.2.50
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(ED3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ECDH1_0923
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	469008
	Strain	:	BL21(DE3)
	Synonym	:	6-CARBOXYTERAHYDROPTERIN SYNTHASE, PTPS

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 12)

No.	Name	Count	Type	Full Name
1	BIO	6	Ligand/Ion	BIOPTERIN
2	ZN	6	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:15 , LEU A:17 , LYS A:25 , ALA A:26 , HIS A:30 , HIS A:32 , THR A:83 , SER A:84 , GLU A:85 , GLU A:109 , ZN A:122 , LEU B:5 , TRP B:50 , ILE B:52 , ASP B:53 , PHE B:54 , HIS D:70	BINDING SITE FOR RESIDUE BIO A 121
02	AC2	SOFTWARE	HIS A:15 , HIS A:30 , HIS A:32 , BIO A:121	BINDING SITE FOR RESIDUE ZN A 122
03	AC3	SOFTWARE	HIS B:15 , LYS B:25 , ALA B:26 , HIS B:30 , HIS B:32 , THR B:83 , SER B:84 , GLU B:85 , GLU B:109 , ZN B:122 , LEU C:5 , TRP C:50 , ILE C:52 , ASP C:53 , PHE C:54 , HIS F:70	BINDING SITE FOR RESIDUE BIO B 121
04	AC4	SOFTWARE	HIS B:15 , HIS B:30 , HIS B:32 , BIO B:121	BINDING SITE FOR RESIDUE ZN B 122
05	AC5	SOFTWARE	TRP A:50 , ILE A:52 , ASP A:53 , PHE A:54 , HIS C:15 , LEU C:17 , ALA C:26 , HIS C:30 , HIS C:32 , THR C:83 , SER C:84 , GLU C:85 , GLU C:109 , ZN C:122 , HIS E:70	BINDING SITE FOR RESIDUE BIO C 121
06	AC6	SOFTWARE	HIS C:15 , HIS C:30 , HIS C:32 , BIO C:121	BINDING SITE FOR RESIDUE ZN C 122
07	AC7	SOFTWARE	HIS A:70 , HIS D:15 , LYS D:25 , ALA D:26 , HIS D:30 , HIS D:32 , THR D:83 , SER D:84 , GLU D:85 , GLU D:109 , ZN D:122 , LEU E:5 , TRP E:50 , ILE E:52 , ASP E:53 , PHE E:54	BINDING SITE FOR RESIDUE BIO D 121
08	AC8	SOFTWARE	HIS D:15 , HIS D:30 , HIS D:32 , BIO D:121	BINDING SITE FOR RESIDUE ZN D 122
09	AC9	SOFTWARE	HIS C:70 , HIS E:15 , ALA E:26 , HIS E:30 , HIS E:32 , THR E:83 , SER E:84 , GLU E:85 , GLU E:109 , ZN E:122 , TRP F:50 , ILE F:52 , ASP F:53 , PHE F:54	BINDING SITE FOR RESIDUE BIO E 121
10	BC1	SOFTWARE	HIS E:15 , HIS E:30 , HIS E:32 , BIO E:121	BINDING SITE FOR RESIDUE ZN E 122
11	BC2	SOFTWARE	HIS B:70 , LEU D:5 , TRP D:50 , ILE D:52 , ASP D:53 , PHE D:54 , HIS F:15 , LEU F:17 , LYS F:25 , ALA F:26 , HIS F:30 , HIS F:32 , THR F:83 , SER F:84 , GLU F:85 , GLU F:109 , ZN F:122	BINDING SITE FOR RESIDUE BIO F 121
12	BC3	SOFTWARE	HIS F:15 , HIS F:30 , HIS F:32 , GLU F:109 , BIO F:121	BINDING SITE FOR RESIDUE ZN F 122

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

(no "Cis Peptide Bond" information available for 3QNA)

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

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

(no "Exon" information available for 3QNA)

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:118
 aligned with QUED_ECOLI | P65870 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:118
                                    12        22        32        42        52        62        72        82        92       102       112        
           QUED_ECOLI     3 STTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 120
               SCOP domains d3qnaa_ A: automated matches                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhh.eeeeeeeeeeeee..........hhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3qna A   2 STTLFKDFTFEAAHRLPHVPEGHKAGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 119
                                    11        21        31        41        51        61        71        81        91       101       111

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with QUED_ECOLI | P65870 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:118
                                    12        22        32        42        52        62        72        82        92       102       112        
           QUED_ECOLI     3 STTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 120
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhh.eeeeeeeeeeee...........hhhhhhhhhhhhhhhhh.ee.hhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3qna B   2 STTLFKDFTFEAAHRLPHVPEGHKAGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 119
                                    11        21        31        41        51        61        71        81        91       101       111

Chain C from PDB  Type:PROTEIN  Length:118
 aligned with QUED_ECOLI | P65870 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:118
                                    12        22        32        42        52        62        72        82        92       102       112        
           QUED_ECOLI     3 STTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 120
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhh.eeeeeeeeeeeee..........hhhhhhhhhhhhhhhhh.ee.hhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3qna C   2 STTLFKDFTFEAAHRLPHVPEGHKAGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 119
                                    11        21        31        41        51        61        71        81        91       101       111

Chain D from PDB  Type:PROTEIN  Length:118
 aligned with QUED_ECOLI | P65870 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:118
                                    12        22        32        42        52        62        72        82        92       102       112        
           QUED_ECOLI     3 STTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 120
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhh.eeeeeeeeeeee...........hhhhhhhhhhhhhhhhh.ee.hhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3qna D   2 STTLFKDFTFEAAHRLPHVPEGHKAGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 119
                                    11        21        31        41        51        61        71        81        91       101       111

Chain E from PDB  Type:PROTEIN  Length:118
 aligned with QUED_ECOLI | P65870 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:118
                                    12        22        32        42        52        62        72        82        92       102       112        
           QUED_ECOLI     3 STTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 120
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhh.eeeeeeeeeeeee..........hhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3qna E   2 STTLFKDFTFEAAHRLPHVPEGHKAGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 119
                                    11        21        31        41        51        61        71        81        91       101       111

Chain F from PDB  Type:PROTEIN  Length:118
 aligned with QUED_ECOLI | P65870 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:118
                                    12        22        32        42        52        62        72        82        92       102       112        
           QUED_ECOLI     3 STTLFKDFTFEAAHRLPHVPEGHKCGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 120
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........hhhhh.eeeeeeeeeeeee..........hhhhhhhhhhhhhhhhh.ee.hhh......hhhhhhhhhhhhhh.....eeeeeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3qna F   2 STTLFKDFTFEAAHRLPHVPEGHKAGRLHGHSFMVRLEITGEVDPHTGWIIDFAELKAAFKPTYERLDHHYLNDIPGLENPTSEVLAKWIWDQVKPVVPLLSAVMVKETCTAGCIYRG 119
                                    11        21        31        41        51        61        71        81        91       101       111

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: T-fold (116)

Superfamily: Tetrahydrobiopterin biosynthesis enzymes-like (113)

Family: automated matches (13)

Protein domain: automated matches (13)

Escherichia coli [TaxId: 469008] (3)

d3qnaa_

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E,F (QUED_ECOLI | P65870)

molecular function
	GO:0070497	6-carboxy-5,6,7,8-tetrahydropterin synthase activity	Catalysis of the reaction: 7,8-dihydroneopterin triphosphate + H2O = 6-carboxy-5,6,7,8-tetrahydropterin + triphosphate + acetaldehyde + 2 H+.
	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:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0008616	queuosine biosynthetic process	The chemical reactions and pathways resulting in the formation of queuosines, any of a series of nucleosides found in tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3qna)

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	3qna
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	QUED_ECOLI \| P65870
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	4.1.2.50
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	QUED_ECOLI \| P65870	:	3qn0 3qn9 4ntk 4ntm 4ntn

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (6, 6)

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