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Title :   PHOSPHOKETOLASE FROM BIFIDOBACTERIUM BREVE COMPLEXED WITH DIHYDROXYETHYL THIAMINE DIPHOSPHATE

Authors :   R. Suzuki, T. Katayama, B. -J. Kim, T. Wakagi, H. Shoun, H. Ashida, K. Yam S. Fushinobu

Date :   22 Apr 10 (Deposition) - 25 Aug 10 (Release) - 03 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Thiamine Diphosphate-Dependent Enzyme, Alpha-Beta Fold, Homodimer, Dihydroxyethyl Thiamine Diphosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Suzuki, T. Katayama, B. -J. Kim, T. Wakagi, H. Shoun, H. Ashida, K. Yamamoto, S. Fushinobu
Crystal Structures Of Phosphoketolase: Thiamine Diphosphate-Dependent Dehydration Mechanism
J. Biol. Chem. V. 285 34279 2010
PubMed-ID: 20739284 | Reference-DOI: 10.1074/JBC.M110.156281
(for further references see the PDB file header)

Molecule 1 - XYLULOSE 5-PHOSPHATE/FRUCTOSE 6-PHOSPHATE PHOSPHOKETOLASE
	Chains	:	A
	EC Number	:	4.1.2.22
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21 CODONPLUS(DE3)-RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	XFP
	Organism Scientific	:	BIFIDOBACTERIUM BREVE
	Organism Taxid	:	1685
	Strain	:	203
	Synonym	:	PHOSPHOKETOLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 15)

No.	Name	Count	Type	Full Name
1	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
2	EDO	11	Ligand/Ion	1,2-ETHANEDIOL
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	NA	1	Ligand/Ion	SODIUM ION
5	THD	1	Ligand/Ion	2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYLTRIHYDROGEN DIPHOSPHATE

Biological Unit 1 (3, 26)

No.	Name	Count	Type	Full Name
1	2PE	2	Ligand/Ion	NONAETHYLENE GLYCOL
2	EDO	22	Ligand/Ion	1,2-ETHANEDIOL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NA	-1	Ligand/Ion	SODIUM ION
5	THD	2	Ligand/Ion	2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYLTRIHYDROGEN DIPHOSPHATE

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:182 , ASN A:215 , TYR A:217 , THD A:827 , HOH A:1240	BINDING SITE FOR RESIDUE MG A 826
02	AC2	SOFTWARE	THR A:67 , HIS A:97 , HIS A:142 , GLY A:155 , LEU A:157 , GLY A:181 , ASP A:182 , GLY A:183 , GLU A:184 , ASN A:215 , TYR A:217 , LYS A:218 , ILE A:219 , LYS A:300 , HIS A:320 , ASP A:436 , GLU A:437 , LEU A:477 , GLU A:479 , TYR A:501 , PHE A:504 , ASN A:549 , HIS A:553 , MG A:826 , HOH A:890 , HOH A:1240 , HOH A:1489 , HOH A:1614	BINDING SITE FOR RESIDUE THD A 827
03	AC3	SOFTWARE	HIS A:726 , ASP A:727 , HOH A:1521	BINDING SITE FOR RESIDUE NA A 828
04	AC4	SOFTWARE	ASN A:637 , ASP A:638 , THR A:700 , ALA A:701 , ASP A:702 , HOH A:1443	BINDING SITE FOR RESIDUE EDO A 829
05	AC5	SOFTWARE	GLU A:627 , ALA A:634 , ASN A:636 , ASN A:637 , LYS A:670	BINDING SITE FOR RESIDUE EDO A 830
06	AC6	SOFTWARE	ASN A:45 , LYS A:49 , HOH A:1434 , HOH A:1496	BINDING SITE FOR RESIDUE EDO A 831
07	AC7	SOFTWARE	ASP A:230 , HOH A:1023	BINDING SITE FOR RESIDUE EDO A 832
08	AC8	SOFTWARE	GLN A:127 , ARG A:131 , HOH A:1404	BINDING SITE FOR RESIDUE EDO A 833
09	AC9	SOFTWARE	ARG A:524 , GLU A:525 , GLY A:738	BINDING SITE FOR RESIDUE EDO A 834
10	BC1	SOFTWARE	THR A:283 , LYS A:312 , GLU A:314	BINDING SITE FOR RESIDUE EDO A 835
11	BC2	SOFTWARE	ARG A:297 , HOH A:1510	BINDING SITE FOR RESIDUE EDO A 836
12	BC3	SOFTWARE	LEU A:777 , GLU A:797 , HOH A:1422 , HOH A:1546	BINDING SITE FOR RESIDUE EDO A 837
13	BC4	SOFTWARE	ALA A:220 , TRP A:317 , LYS A:452 , VAL A:463 , ASP A:464 , GLU A:465 , MET A:467	BINDING SITE FOR RESIDUE EDO A 838
14	BC5	SOFTWARE	THR A:566 , PHE A:567 , GLN A:681 , ARG A:717 , HOH A:1128 , HOH A:1505	BINDING SITE FOR RESIDUE EDO A 839
15	BC6	SOFTWARE	GLN A:321 , ARG A:442 , ASP A:547 , HIS A:548 , HOH A:1213 , HOH A:1400	BINDING SITE FOR RESIDUE 2PE A 840

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

Asymmetric Unit

No.	Residues
1	Glu A:50	-	Pro A:51

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

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

(no "Exon" information available for 3AHE)

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:802
 aligned with D6PAH1_BIFBR | D6PAH1 from UniProtKB/TrEMBL  Length:825

    Alignment length:802
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804  
         D6PAH1_BIFBR     5 VIGTPWQKLDRPVSEEAIEGMDKYWRVTNYMSIGQIYLRSNPLMKEPFTRDDVKHRLVGHWGTTPGLNFLLAHINRLIADHQQNTVFIMGPGHGGPAGTSQSYVDGTYTEYYPNITKDEAGLQKFFRQFSYPGGIPSHFAPETPGSIHEGGELGYALSHAYGAVMNNPSLFVPCIIGDGEAETGPLATGWQSNKLVNPRTDGIVLPILHLNGYKIANPTILARISDEELHDFFRGMGYHPYEFVAGFDNEDHMSIHRRFAELFETIFDEICDIKAAAQTDDMTRPFYPMLIFRTPKGWTCPKFIDGKKTEGSWRAHQVPLASARDTEEHFEVLKGWMESYKPEELFNADGSIKDDVTAFMPKGELRIGANPNANGGVIREDLKLPELDQYEVTGVKEYGHGWGQVEAPRALGAYCRDIIKNNPDSFRIFGPDETASNRLNATYEVTDKQWDNGYLSGLVDEHMAVTGQVTEQLSEHQCEGFLEAYLLTGRHGIWSSYESFVHVIDSMLNQHAKWLEATVREIPWRKPISSVNLLVSSHVWRQDHNGFSHQDPGVTSLLINKTFNNDHVTNIYFATDANMLLAISEKCFKSTNKINAIFAGKQPAPTWVTLDEARAELEAGAAEWKWASNAENNDEVQVVLASAGDVPTQELMAASDALNKMGIKFKVVNVVDLLKLQSRENNDEALTDEEFTELFTADKPVLFAYHSYAQDVRGLIYDRPNHDNFHVVGYKEQGSTTTPFDMVRVNDMDRYALQAAALKLIDADKYADKIDELNAFRKKAFQFAVDNGYDIPEFTDWVYPDV 806
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh.........hhhhhhhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.........................hhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhh.......eeeeeeee........hhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.........ee..ee...hhhhh.........hhhhhhhhhhhhhhhhhhhh.......hhhhhh...hhhhh...hhhhhhhhh.......hhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhh...eeeee........hhhhhhh..ee.............ee....eee..hhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh........eeeeee.........hhhhh..hhhhhhh.........eeeee..hhhhhhhhhhhhhhh...eeeee....eeee..hhhhhhhhhhhheee........hhhhh.eeeeeehhhhhhhhhhhhhhhhhh...eeeeee.hhhhhh.........hhhhhhhhhh....eeeee...hhhhhhhh....hhh.eeee.........hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ahe A   5 VIGTPWQKLDRPVSEEAIEGMDKYWRVTNYMSIGQIYLRSNPLMKEPFTRDDVKHRLVGHWGTTPGLNFLLAHINRLIADHQQNTVFIMGPGHGGPAGTSQSYVDGTYTEYYPNITKDEAGLQKFFRQFSYPGGIPSHFAPETPGSIHEGGELGYALSHAYGAVMNNPSLFVPCIIGDGEAETGPLATGWQSNKLVNPRTDGIVLPILHLNGYKIANPTILARISDEELHDFFRGMGYHPYEFVAGFDNEDHMSIHRRFAELFETIFDEICDIKAAAQTDDMTRPFYPMLIFRTPKGWTCPKFIDGKKTEGSWRAHQVPLASARDTEEHFEVLKGWMESYKPEELFNADGSIKDDVTAFMPKGELRIGANPNANGGVIREDLKLPELDQYEVTGVKEYGHGWGQVEAPRALGAYCRDIIKNNPDSFRIFGPDETASNRLNATYEVTDKQWDNGYLSGLVDEHMAVTGQVTEQLSEHQCEGFLEAYLLTGRHGIWSSYESFVHVIDSMLNQHAKWLEATVREIPWRKPISSVNLLVSSHVWRQDHNGFSHQDPGVTSLLINKTFNNDHVTNIYFATDANMLLAISEKCFKSTNKINAIFAGKQPAPTWVTLDEARAELEAGAAEWKWASNAENNDEVQVVLASAGDVPTQELMAASDALNKMGIKFKVVNVVDLLKLQSRENNDEALTDEEFTELFTADKPVLFAYHSYAQDVRGLIYDRPNHDNFHVVGYKEQGSTTTPFDMVRVNDMDRYALQAAALKLIDADKYADKIDELNAFRKKAFQFAVDNGYDIPEFTDWVYPDV 806
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804

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 '\|'

(no "SCOP Domain" information available for 3AHE)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (D6PAH1_BIFBR | D6PAH1)

molecular function
	GO:0016832	aldehyde-lyase activity	Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
	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: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:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:50 - Pro A:51	[ RasMol ]

Biological Unit
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	3ahe
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	D6PAH1_BIFBR \| D6PAH1
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	4.1.2.22
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UniProtKB/TrEMBL
	D6PAH1_BIFBR \| D6PAH1	:	3ahc 3ahd 3ahf 3ahg 3ahh 3ahi 3ahj

3ahc	LIGAND-FREE FORM OF THE SAME PROTEIN
3ahd	THE SAME PROTEIN COMPLEXED WITH 2-ACETYL-THIAMINE DIPHOSPHATE
3ahf	THE SAME PROTEIN COMPLEXED WITH INORGANIC PHOSPHATE
3ahg	H64A MUTATION OF THE SAME PROTEIN COMPLEXED WITH DIHYDROTHIACHROMINE FORM OF THIAMINE DIPHOSPHATE
3ahh	H142A MUTATION OF THE SAME PROTEIN COMPLEXED WITH ACETYL THIAMINE DIPHOSPHATE
3ahi	H320A MUTATION OF THE SAME PROTEIN COMPLEXED WITH ACETYL THIAMINE DIPHOSPHATE
3ahj	H553A MUTATION OF THE SAME PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File