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Title :   THE STRUCTURE OF 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH PHENYLALANINE

Authors :   E. J. Parker, G. B. Jameson, W. Jiao, C. J. Webby, E. N. Baker, H. M. Baker

Date :   06 Jul 10 (Deposition) - 28 Jul 10 (Release) - 22 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Mycobacterium Tuberculosis, Dah7P Synthase, Shikimate Pathway, Aromatic Biosynthesis, Evolutionary Relationships, Transferase, Phe- Bound, Augmented Tim-Barrel Structure (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. J. Webby, W. Jiao, R. D. Hutton, N. J. Blackmore, H. M. Baker, E. N. Baker, G. B. Jameson, E. J. Parker
Synergistic Allostery, A Sophisticated Regulatory Network For The Control Of Aromatic Amino Acid Biosynthesis In Mycobacterium Tuberculosis
J. Biol. Chem. V. 285 30567 2010
PubMed-ID: 20667835 | Reference-DOI: 10.1074/JBC.M110.111856

Molecule 1 - PROBABLE 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE AROG
	Chains	:	A, B
	EC Number	:	2.5.1.54
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPROEXHTA
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RV2178C
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Strain	:	H37RV
	Synonym	:	DAHP SYNTHETASE, PHENYLALANINE-REPRESSIBLE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	PHE	5	Mod. Amino Acid	PHENYLALANINE
2	PO4	5	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 20)

No.	Name	Count	Type	Full Name
1	PHE	10	Mod. Amino Acid	PHENYLALANINE
2	PO4	10	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:91 , ARG A:171 , ALA A:174 , ASN A:175	BINDING SITE FOR RESIDUE PHE A 465
02	AC2	SOFTWARE	GLY A:282 , GLU A:283 , LYS A:306 , ARG A:337 , HIS A:369 , HOH A:468	BINDING SITE FOR RESIDUE PO4 A 463
03	AC3	SOFTWARE	LEU A:107 , VAL A:111 , LYS A:123 , ALA A:192 , ASN A:237 , LEU A:238 , GLN A:239 , THR A:240 , ALA A:241	BINDING SITE FOR RESIDUE PHE A 466
04	AC4	SOFTWARE	ARG A:135 , SER A:136 , ALA A:137 , ARG A:284	BINDING SITE FOR RESIDUE PO4 A 464
05	AC5	SOFTWARE	TYR A:173 , PHE B:91 , ARG B:171 , ALA B:174 , ASN B:175	BINDING SITE FOR RESIDUE PHE B 466
06	AC6	SOFTWARE	VAL B:111 , LYS B:123 , ALA B:192 , LEU B:194 , CYS B:231 , ASN B:237 , GLN B:239 , ALA B:241	BINDING SITE FOR RESIDUE PHE B 467
07	AC7	SOFTWARE	ARG B:23 , GLU B:53 , ARG B:256 , LEU B:259	BINDING SITE FOR RESIDUE PHE B 468
08	AC8	SOFTWARE	GLY B:282 , GLU B:283 , LYS B:306 , ARG B:337 , HIS B:369	BINDING SITE FOR RESIDUE PO4 B 463
09	AC9	SOFTWARE	ARG B:135 , SER B:136 , ALA B:137 , ARG B:284	BINDING SITE FOR RESIDUE PO4 B 464
10	BC1	SOFTWARE	PRO B:17 , LEU B:18 , ARG B:23 , ASP B:158 , ALA B:159	BINDING SITE FOR RESIDUE PO4 B 465

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

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

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

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

(no "Exon" information available for 3NUD)

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:442
 aligned with AROG_MYCTU | O53512 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:462
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     462  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462  
           AROG_MYCTU     3 WTVDIPIDQLPSLPPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMPVVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQTAEIYASHEALVLDYERAMLRLSDGDDGEPQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKVQATGHQVIWQCDPMHGNTHESSTGFKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVTECLGGAQDISETDLAGRYETACDPRLNTQQSLELAFLVAEMLRD--   -
               SCOP domains d3nuda_    A: Probable DAHP synthetase AroG, phenylalanine-repressible                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..---......hhhhhhhhhhhhh.........hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.......................................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...........eeeeee..hhhhhhhheee.........eee....eeeehhhhh...hhhhhhhhhh...eeeee....hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhhhhh.....eeee.................hhhhhhhhhhhhhhhhhhhh....eeeee.......-----------------.........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nud A   3 WTVDIPI---PSLPPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMPVVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQTAEIYASHEALVLDYERAMLRLSDGDDGEPQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKVQATGHQVIWQCDPMHGNTHESSTGFKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVT-----------------YETACDPRLNTQQSLELAFLVAEMLRDFF 466
                                  |  -|       22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412     |   -         -   |   442       452       462| 
                                  9  13                                                                                                                                                                                                                                                                                                                                                                                                                  418               436                       462| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      465

Chain B from PDB  Type:PROTEIN  Length:444
 aligned with AROG_MYCTU | O53512 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:467
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                          462   
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458   |   
           AROG_MYCTU     - --MNWTVDIPIDQLPSLPPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMPVVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQTAEIYASHEALVLDYERAMLRLSDGDDGEPQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKVQATGHQVIWQCDPMHGNTHESSTGFKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVTECLGGAQDISETDLAGRYETACDPRLNTQQSLELAFLVAEMLRD---   -
               SCOP domains d3nudb_ B:       Probable DAHP synthetase AroG, phenylalanine-repressible                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...------...hhhhhhhhhhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...............................hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..hhhhh....eeeeee..hhhhhhhheee.........eee.....eeehhhhh...hhhhhhhhhh...eeeee....hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhhhhh.....eeee..........---....hhhhhhhhhhhhhhhhhhhh....eeeee.......--------------............hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nud B  -1 GAMNWTVDIPI------PPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMPVVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQTAEIYASHEALVLDYERAMLRLSDGDDGEPQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKVQATGHQVIWQCDPMHGNTHES---FKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVT--------------AGRYETACDPRLNTQQSLELAFLVAEMLRDFFF 468
                                     8|      |18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368      |  -|      388       398       408       418         -    |  438       448       458   ||  
                                      9     16                                                                                                                                                                                                                                                                                                                                                                    375 379                                    418            433                          462|  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          466

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: Class-II DAHP synthetase (13)

Protein domain: Probable DAHP synthetase AroG, phenylalanine-repressible (5)

Mycobacterium tuberculosis [TaxId: 1773] (5)

1a	d3nuda_	A:
1b	d3nudb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (AROG_MYCTU | O53512)

molecular function
	GO:0003849	3-deoxy-7-phosphoheptulonate synthase activity	Catalysis of the reaction: D-erythrose 4-phosphate + H(2)O + phosphoenolpyruvate = 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate + phosphate.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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.
biological process
	GO:0009073	aromatic amino acid family biosynthetic process	The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0009423	chorismate biosynthetic process	The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3nud)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3nud
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	2.5.1.54
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2b7o	THE SAME PROTEIN WITHOUT PHENYLALANINE
3kgf	THE SAME PROTEIN WITH BOTH TRYPTOPHAN AND PHENYLALANINE BOUND
3nue	THE SAME PROTEIN WITH TRYPTOPHAN BOUND IN ONLY THE TRYPTOPHAN-BINDING SITE
3nv8	THE SAME PROTEIN WITH PHOSPHOENOL PYRUVATE AND MANGANESE (THESIT-FREE)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

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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SCOP Domains (1, 2)

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Gene Ontology (13, 13)

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