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Title :   THE STRUCTURE OF 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE IN COMPLEX WITH PHOSPHOENOL PYRUVATE AND MANGANESE (THESIT-FREE)

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

Date :   08 Jul 10 (Deposition) - 28 Jul 10 (Release) - 22 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Dah7P Synthase, Shikimate Pathway, Aromatic Amino-Acid Biosynthesis, Evolutionary Relationships, Augmented Tim-Barrel Structure, Tim Barrel, Aldolase, Cytosol, Transferase (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
(for further references see the PDB file header)

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 (6, 14)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GOL	6	Ligand/Ion	GLYCEROL
3	MN	2	Ligand/Ion	MANGANESE (II) ION
4	PEP	1	Ligand/Ion	PHOSPHOENOLPYRUVATE
5	PO4	1	Ligand/Ion	PHOSPHATE ION
6	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 22)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	12	Ligand/Ion	GLYCEROL
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	PEP	2	Ligand/Ion	PHOSPHOENOLPYRUVATE
5	PO4	2	Ligand/Ion	PHOSPHATE ION
6	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:138 , ARG A:145 , ARG A:148 , HIS A:164 , HOH A:549 , HOH A:597	BINDING SITE FOR RESIDUE SO4 A 463
02	AC2	SOFTWARE	CYS A:87 , HIS A:369 , GLU A:411 , ASP A:441	BINDING SITE FOR RESIDUE MN A 464
03	AC3	SOFTWARE	ARG A:168 , ARG A:171 , PRO B:8	BINDING SITE FOR RESIDUE GOL A 465
04	AC4	SOFTWARE	ARG A:171 , ALA A:174 , ASN A:175 , ILE B:7	BINDING SITE FOR RESIDUE GOL A 466
05	AC5	SOFTWARE	ARG A:126 , GLU A:248 , TRP A:280 , GLY A:282 , GLU A:283 , LYS A:306 , ARG A:337 , HIS A:369	BINDING SITE FOR RESIDUE PEP A 467
06	AC6	SOFTWARE	ARG B:23 , LEU B:26 , ARG B:49 , ARG B:256 , HOH B:502 , HOH B:600	BINDING SITE FOR RESIDUE SO4 B 463
07	AC7	SOFTWARE	ARG B:135 , SER B:136 , ALA B:137 , ARG B:284	BINDING SITE FOR RESIDUE SO4 B 464
08	AC8	SOFTWARE	CYS B:87 , HIS B:369 , GLU B:411 , ASP B:441	BINDING SITE FOR RESIDUE MN B 465
09	AC9	SOFTWARE	THR B:114 , VAL B:121 , LYS B:123 , LEU B:194	BINDING SITE FOR RESIDUE GOL B 466
10	BC1	SOFTWARE	GLN B:70 , VAL B:121 , VAL B:122 , LYS B:123 , GLU B:242 , HOH B:516 , HOH B:573	BINDING SITE FOR RESIDUE GOL B 467
11	BC2	SOFTWARE	PRO B:17 , LEU B:18 , ARG B:23 , LEU B:144 , ALA B:159	BINDING SITE FOR RESIDUE GOL B 468
12	BC3	SOFTWARE	ARG B:25 , ALA B:294 , GLN B:297 , VAL B:298 , HOH B:610 , HOH B:613	BINDING SITE FOR RESIDUE GOL B 469
13	BC4	SOFTWARE	ARG B:49 , HOH B:504 , HOH B:612	BINDING SITE FOR RESIDUE CL B 470
14	BC5	SOFTWARE	GLY B:282 , GLU B:283 , LYS B:306 , ARG B:337 , HIS B:369	BINDING SITE FOR RESIDUE PO4 B 471

(no "SS Bond" information available for 3NV8)

(no "Cis Peptide Bond" information available for 3NV8)

(no "SAP(SNP)/Variant" information available for 3NV8)

(no "PROSITE Motif" information available for 3NV8)

(no "Exon" information available for 3NV8)

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

    Alignment length:462
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460  
           AROG_MYCTU     1 MNWTVDIPIDQLPSLPPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMPVVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQTAEIYASHEALVLDYERAMLRLSDGDDGEPQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKVQATGHQVIWQCDPMHGNTHESSTGFKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVTECLGGAQDISETDLAGRYETACDPRLNTQQSLELAFLVAEMLRD 462
               SCOP domains d3nv8a_ A: Probable DAHP synthetase AroG, phenylalanine-repressible                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee..........hhhhhhhhhhhh..........hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...............................hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhh....eeeeee..hhhhhhhheee.........eee....eeee........hhhhhhhhhh...eeeee....hhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhhhh.....eeee......eee.....eeehhhhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhh..........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nv8 A   1 MNWTVDIPIDQLPSLPPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMPVVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQTAEIYASHEALVLDYERAMLRLSDGDDGEPQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKVQATGHQVIWQCDPMHGNTHESSTGFKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVTECLGGAQDISETDLAGRYETACDPRLNTQQSLELAFLVAEMLRD 462
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460

Chain B from PDB  Type:PROTEIN  Length:464
 aligned with AROG_MYCTU | O53512 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:464
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
                              |      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 462
               SCOP domains d3nv8b_ B: Probable DAHP synthetase AroG, phenylalanine-repressible                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeee..........hhhhhhhhhhhhh.........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee................................hhhhh..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhh....eeeeee..hhhhhhhheee.........eee....eeee........hhhhhhhh.....eeeee....hhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhhhhh....eeee......eee.....eeehhhhhhhhhhhhhhhhhhhh..eeeeeee.................hhhhhh..........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nv8 B  -1 GAMNWTVDIPIDQLPSLPPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMPVVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQTAEIYASHEALVLDYERAMLRLSDGDDGEPQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKVQATGHQVIWQCDPMHGNTHESSTGFKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVTECLGGAQDISETDLAGRYETACDPRLNTQQSLELAFLVAEMLRD 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

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: Aldolase (457)

Family: Class-II DAHP synthetase (13)

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

Mycobacterium tuberculosis [TaxId: 1773] (5)

1a	d3nv8a_	A:
1b	d3nv8b_	B:

(no "CATH Domain" information available for 3NV8)

(no "Pfam Domain" information available for 3NV8)

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 3nv8)

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	3nv8
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2b7o	THE SAME PROTEIN BUT WITH THESIT PRESENT
3kgf	THE SAME PROTEIN WITH BOTH TRYPTOPHAN AND PHENYLALANINE BOUND
3nud	THE SAME PROTEIN WITH PHENYLALANINE BOUND IN PHENYLALANINE- AND TRYPTOPHAN-BINDING SITES
3nue	THE SAME PROTEIN WITH TRYPTOPHAN BOUND IN ONLY THE TRYPTOPHAN-BINDING SITE

Description

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Ligands, Modified Residues, Ions (6, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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