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Title :   CRYSTAL STRUCTURE OF PREPHENATE DEHYDROGENASE FROM A. AEOLICUS IN COMPLEX WITH HYDROXYPHENYL PROPIONATE AND NAD+

Authors :   W. Sun, D. Shahinas, M. S. Kimber, D. Christendat

Date :   01 Mar 09 (Deposition) - 10 Mar 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Hydroxyphenyl Propionate, Tyra, Prephenate Dehydrogenase, Alpha-Beta, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Sun, D. Shahinas, J. Bonvin, W. Hou, M. S. Kimber, J. Turnbull, D. Christendat
The Crystal Structure Of Aquifex Aeolicus Prephenate Dehydrogenase Reveals The Mode Of Tyrosine Inhibition.
J. Biol. Chem. V. 284 13223 2009
PubMed-ID: 19279014 | Reference-DOI: 10.1074/JBC.M806272200

Molecule 1 - PREPHENATE DEHYDROGENASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AQ_1755, TYRA
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Strain	:	VF5

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	HPP	2	Ligand/Ion	HYDROXYPHENYL PROPIONIC ACID
3	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	HPP	1	Ligand/Ion	HYDROXYPHENYL PROPIONIC ACID
3	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	HPP	1	Ligand/Ion	HYDROXYPHENYL PROPIONIC ACID
3	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:37 , VAL A:38 , GLY A:39 , PHE A:40 , MET A:41 , TYR A:61 , ASP A:62 , ILE A:63 , SER A:67 , SER A:98 , SER A:99 , PRO A:100 , VAL A:101 , THR A:103 , GLN A:124 , GLY A:125 , SER A:126 , PRO A:148 , ALA A:150 , GLY A:151 , SER A:155 , GLY A:156 , GLU A:234 , MET A:258 , HOH A:1027	BINDING SITE FOR RESIDUE NAD A 312
2	AC2	SOFTWARE	TYR A:240 , PRO A:241 , GLY A:242 , ILE C:149 , LYS C:169 , HOH C:1009	BINDING SITE FOR RESIDUE CL A 313
3	AC3	SOFTWARE	GLY B:37 , VAL B:38 , GLY B:39 , PHE B:40 , MET B:41 , ASP B:62 , ILE B:63 , ASN B:64 , SER B:67 , SER B:98 , SER B:99 , PRO B:100 , VAL B:101 , ILE B:107 , GLN B:124 , SER B:126 , PRO B:148 , ALA B:150 , GLY B:151 , THR B:152 , SER B:155 , GLY B:156 , MET B:258 , HPP B:313 , HOH B:1001 , HOH B:1013 , HOH B:1015 , HOH B:1030 , HOH B:1054 , HOH B:1413	BINDING SITE FOR RESIDUE NAD B 312
4	AC4	SOFTWARE	SER B:126 , HIS B:147 , ALA B:150 , GLY B:151 , THR B:152 , GLU B:153 , ARG B:250 , ILE B:251 , NAD B:312 , HOH B:1003 , HOH B:1028 , HOH B:1058 , HOH B:1064 , GLY D:242 , GLY D:243 , GLY D:244	BINDING SITE FOR RESIDUE HPP B 313
5	AC5	SOFTWARE	LYS B:169 , HOH B:1420 , GLY D:242	BINDING SITE FOR RESIDUE CL B 314
6	AC6	SOFTWARE	GLY C:37 , VAL C:38 , GLY C:39 , PHE C:40 , MET C:41 , ASP C:62 , ILE C:63 , ASN C:64 , SER C:67 , SER C:98 , SER C:99 , PRO C:100 , VAL C:101 , THR C:103 , ILE C:107 , GLN C:124 , SER C:126 , PRO C:148 , ALA C:150 , GLY C:151 , THR C:152 , SER C:155 , GLY C:156 , MET C:258 , HPP C:313 , HOH C:1012 , HOH C:1024 , HOH C:1042 , HOH C:1415	BINDING SITE FOR RESIDUE NAD C 312
7	AC7	SOFTWARE	GLY A:242 , GLY A:243 , GLY A:244 , HOH A:1034 , SER C:126 , HIS C:147 , ALA C:150 , THR C:152 , GLU C:153 , ARG C:250 , ILE C:251 , MET C:258 , NAD C:312 , HOH C:1005 , HOH C:1007	BINDING SITE FOR RESIDUE HPP C 313
8	AC8	SOFTWARE	GLY D:37 , VAL D:38 , GLY D:39 , PHE D:40 , MET D:41 , TYR D:61 , ASP D:62 , ILE D:63 , SER D:67 , SER D:98 , SER D:99 , PRO D:100 , VAL D:101 , THR D:103 , ILE D:107 , GLN D:124 , SER D:126 , THR D:152 , GLU D:153 , GLY D:156 , HOH D:1101	BINDING SITE FOR RESIDUE NAD D 312

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

Asymmetric Unit

No.	Residues
1	Ser D:29	-	Met D:30

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

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

(no "Exon" information available for 3GGP)

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:286
 aligned with O67636_AQUAE | O67636 from UniProtKB/TrEMBL  Length:311

    Alignment length:286
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305      
         O67636_AQUAE    26 KSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRMEID 311
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh....eee..hhhhhhhh..eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh..ee.eee.......hhhhh........eeee......hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ggp A  26 KSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRMEID 311
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305

Chain B from PDB  Type:PROTEIN  Length:284
 aligned with O67636_AQUAE | O67636 from UniProtKB/TrEMBL  Length:311

    Alignment length:284
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305    
         O67636_AQUAE    26 KSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRME 309
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh....eee.hhhhhhhhh..eeee..hhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhh..ee.eee.......hhhhh........eeee......hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ggp B  26 KSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRME 309
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305

Chain C from PDB  Type:PROTEIN  Length:286
 aligned with O67636_AQUAE | O67636 from UniProtKB/TrEMBL  Length:311

    Alignment length:286
                                    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      
         O67636_AQUAE    25 LKSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRMEI 310
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh....eee....hhhhhh..eeee..hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh..ee.eeee......hhhhh........eeee......hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ggp C  25 LKSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRMEI 310
                                    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

Chain D from PDB  Type:PROTEIN  Length:286
 aligned with O67636_AQUAE | O67636 from UniProtKB/TrEMBL  Length:311

    Alignment length:286
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305      
         O67636_AQUAE    26 KSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRMEID 311
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..hhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh....eee....hhhhhh..eeee..hhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhh..ee.eee.......hhhhh........eeee......hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ggp D  26 KSLSMQNVLIVGVGFMGGSFAKSLRRSGFKGKIYGYDINPESISKAVDLGIIDEGTTSIAKVEDFSPDFVMLSSPVRTFREIAKKLSYILSEDATVTDQGSVKGKLVYDLENILGKRFVGGHPIAGTEKSGVEYSLDNLYEGKKVILTPTKKTDKKRLKLVKRVWEDVGGVVEYMSPELHDYVFGVVSHLPHAVAFALVDTLIHMSTPEVDLFKYPGGGFKDFTRIAKSDPIMWRDIFLENKENVMKAIEGFEKSLNHLKELIVREAEEELVEYLKEVKIKRMEID 311
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305

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 3GGP)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (O67636_AQUAE | O67636)

molecular function
	GO:0070403	NAD+ binding	Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0008977	prephenate dehydrogenase (NAD+) activity	Catalysis of the reaction: NAD(+) + prephenate = (4-hydroxyphenyl)pyruvate + CO(2) + NADH.
	GO:0004665	prephenate dehydrogenase (NADP+) activity	Catalysis of the reaction: NADP(+) + prephenate = (4-hydroxyphenyl)pyruvate + CO(2) + NADPH.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006571	tyrosine biosynthetic process	The chemical reactions and pathways resulting in the formation of tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.

Asymmetric Unit
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	Cis Peptide Bonds
		Ser D:29 - Met D:30	[ RasMol ]

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	O67636_AQUAE \| O67636	:	2g5c 3ggg 3ggo

Description

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Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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