1HO4 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE IN COMPLEX WITH PYRIDOXINE 5'-PHOSPHATE AND INORGANIC PHOSPHATE

Authors :   M. Garrido-Franco, B. Laber, R. Huber, T. Clausen

Date :   08 Dec 00 (Deposition) - 28 Mar 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (2x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: B (1x),C (1x)
Biol. Unit 4: D  (2x)

Keywords :   Tim Barrel, Open-Closed Transition, Enzyme-Product Complex, Water Channel, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. G. Franco, B. Laber, R. Huber, T. Clausen
Structural Basis For The Function Of Pyridoxine 5'-Phosphat Synthase.
Structure V. 9 245 2001
PubMed-ID: 11286891 | Reference-DOI: 10.1016/S0969-2126(01)00584-6

Molecule 1 - PYRIDOXINE 5'-PHOSPHATE SYNTHASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PASK-IBA3
	Expression System Strain	:	JM83
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PDXJ
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PYRIDOXAL PHOSPHATE BIOSYNTHETIC PROTEIN PDXJ

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (2x)	:	A	B	C	D
Biological Unit 2 (2x)	:	A
Biological Unit 3 (1x)	:		B (1x)	C (1x)
Biological Unit 4 (2x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	PO4	3	Ligand/Ion	PHOSPHATE ION
2	PXP	4	Ligand/Ion	PYRIDOXINE-5'-PHOSPHATE

Biological Unit 1 (2, 14)

No.	Name	Count	Type	Full Name
1	PO4	6	Ligand/Ion	PHOSPHATE ION
2	PXP	8	Ligand/Ion	PYRIDOXINE-5'-PHOSPHATE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	PO4	2	Ligand/Ion	PHOSPHATE ION
2	PXP	2	Ligand/Ion	PYRIDOXINE-5'-PHOSPHATE

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION
2	PXP	1	Ligand/Ion	PYRIDOXINE-5'-PHOSPHATE

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	PO4	-1	Ligand/Ion	PHOSPHATE ION
2	PXP	2	Ligand/Ion	PYRIDOXINE-5'-PHOSPHATE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:11 , HIS A:12 , ARG A:20 , HIS A:45 , ARG A:47 , HIS A:52 , THR A:102 , PXP A:802 , HOH A:972 , HOH A:993 , HOH A:1093	BINDING SITE FOR RESIDUE PO4 A 901
2	AC2	SOFTWARE	ARG B:20 , ASP C:11 , HIS C:12 , HIS C:45 , ARG C:47 , HIS C:52 , THR C:102 , PXP C:803 , HOH C:1075 , HOH C:1084	BINDING SITE FOR RESIDUE PO4 C 902
3	AC3	SOFTWARE	ASP B:11 , HIS B:12 , HIS B:45 , ARG B:47 , HIS B:52 , THR B:102 , PXP B:804 , HOH B:956 , HOH B:1070 , ARG C:20	BINDING SITE FOR RESIDUE PO4 B 903
4	AC4	SOFTWARE	ASN D:9 , ARG D:20 , GLU D:72 , VAL D:94 , PHE D:133 , GLU D:153 , HIS D:193 , GLY D:194 , ASN D:213 , ILE D:214 , GLY D:215 , HIS D:216 , HOH D:816 , HOH D:850 , HOH D:852 , HOH D:969 , HOH D:970 , HOH D:992	BINDING SITE FOR RESIDUE PXP D 801
5	AC5	SOFTWARE	ARG A:20 , GLU A:72 , VAL A:94 , THR A:102 , THR A:103 , PHE A:133 , GLU A:153 , HIS A:193 , GLY A:194 , ASN A:213 , ILE A:214 , GLY A:215 , HIS A:216 , PO4 A:901 , HOH A:956 , HOH A:968 , HOH A:972	BINDING SITE FOR RESIDUE PXP A 802
6	AC6	SOFTWARE	ARG B:20 , GLU C:72 , VAL C:94 , THR C:103 , PHE C:133 , GLU C:153 , HIS C:193 , GLY C:194 , ASN C:213 , ILE C:214 , GLY C:215 , HIS C:216 , PO4 C:902 , HOH C:908 , HOH C:915 , HOH C:966	BINDING SITE FOR RESIDUE PXP C 803
7	AC7	SOFTWARE	GLU B:72 , VAL B:94 , THR B:103 , GLU B:153 , GLY B:192 , HIS B:193 , GLY B:194 , ASN B:213 , ILE B:214 , GLY B:215 , HIS B:216 , PO4 B:903 , HOH B:909 , HOH B:935 , HOH B:956 , ARG C:20	BINDING SITE FOR RESIDUE PXP B 804

(no "SS Bond" information available for 1HO4)

Asymmetric Unit

No.	Residues
1	Tyr A:24	-	Pro A:25
2	Tyr B:24	-	Pro B:25
3	Tyr C:24	-	Pro C:25
4	Tyr D:24	-	Pro D:25

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PDXJ_ECOLI_001 *	G	194	S	PDXJ_ECOLI	---	---	A/B/C/D	G	194	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PDXJ_ECOLI_001 *	G	194	S	PDXJ_ECOLI	---	---	A/B/C/D	G	194	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PDXJ_ECOLI_001 *	G	194	S	PDXJ_ECOLI	---	---	A	G	194	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PDXJ_ECOLI_001 *	G	194	S	PDXJ_ECOLI	---	---	B/C	G	194	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PDXJ_ECOLI_001 *	G	194	S	PDXJ_ECOLI	---	---	D	G	194	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1HO4)

(no "Exon" information available for 1HO4)

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:242
 aligned with PDXJ_ECOLI | P0A794 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
           PDXJ_ECOLI     2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
               SCOP domains d1ho4a_ A: Pyridoxine 5'-phosphate synthase                                                                                                                                                                                                        SCOP domains
               CATH domains 1ho4A00 A:2-243 Aldolase class I                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhh.......hhhhhhhhhhh....eeeee........hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh...eeeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ho4 A   2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain B from PDB  Type:PROTEIN  Length:242
 aligned with PDXJ_ECOLI | P0A794 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
           PDXJ_ECOLI     2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
               SCOP domains d1ho4b_ B: Pyridoxine 5'-phosphate synthase                                                                                                                                                                                                        SCOP domains
               CATH domains 1ho4B00 B:2-243 Aldolase class I                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhhh......hhhhhhhhhhh....eeeee........hhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeee...............hhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh...eeeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ho4 B   2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain C from PDB  Type:PROTEIN  Length:242
 aligned with PDXJ_ECOLI | P0A794 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
           PDXJ_ECOLI     2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
               SCOP domains d1ho4c_ C: Pyridoxine 5'-phosphate synthase                                                                                                                                                                                                        SCOP domains
               CATH domains 1ho4C00 C:2-243 Aldolase class I                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhh.......hhhhhhhhhhh....eeeee........hhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeee..................hhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh...eeeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ho4 C   2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

Chain D from PDB  Type:PROTEIN  Length:242
 aligned with PDXJ_ECOLI | P0A794 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
           PDXJ_ECOLI     2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
               SCOP domains d1ho4d_ D: Pyridoxine 5'-phosphate synthase                                                                                                                                                                                                        SCOP domains
               CATH domains 1ho4D00 D:2-243 Aldolase class I                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhh.......hhhhhhhhhhh....eeeee........hhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeee..................hhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhh..eeeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ho4 D   2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Pyridoxine 5'-phosphate synthase (11)

Family: Pyridoxine 5'-phosphate synthase (8)

Protein domain: Pyridoxine 5'-phosphate synthase (7)

Escherichia coli [TaxId: 562] (7)

1a	d1ho4a_	A:
1b	d1ho4b_	B:
1c	d1ho4c_	C:
1d	d1ho4d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Escherichia coli. Organism_taxid: 562. (43)

1a	1ho4A00	A:2-243
1b	1ho4B00	B:2-243
1c	1ho4C00	C:2-243
1d	1ho4D00	D:2-243

(no "Pfam Domain" information available for 1HO4)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PDXJ_ECOLI | P0A794)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0033856	pyridoxine 5'-phosphate synthase activity	Catalysis of the reaction: 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = 2 H(2)O + H(+) + phosphate + pyridoxine 5'-phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016769	transferase activity, transferring nitrogenous groups	Catalysis of the transfer of a nitrogenous group from one compound (donor) to another (acceptor).
biological process
	GO:0008615	pyridoxine biosynthetic process	The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	1ho4
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	PDXJ_ECOLI \| P0A794	:	1ho1 1ixn 1ixo 1ixp 1ixq 1m5w

1ho1	1HO1 IS THE NATIVE PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 4)

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Exons (0, 0)

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