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(-) Description

Title :  THE STRUCTURE OF 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH TRYPTOPHAN
 
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 :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Mycobacterium Tuberculosis, Dah7P Synthase, Shikimate Pathway, Aromatic Biosynthesis, Evolutionary Relationships, Transferase, Trp- 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

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 19)

Asymmetric Unit (7, 19)
No.NameCountTypeFull Name
1CE11Ligand/IonO-DODECANYL OCTAETHYLENE GLYCOL
2CL1Ligand/IonCHLORIDE ION
3GOL7Ligand/IonGLYCEROL
4MN2Ligand/IonMANGANESE (II) ION
5PO42Ligand/IonPHOSPHATE ION
6SO44Ligand/IonSULFATE ION
7TRP2Mod. Amino AcidTRYPTOPHAN
Biological Unit 1 (5, 32)
No.NameCountTypeFull Name
1CE12Ligand/IonO-DODECANYL OCTAETHYLENE GLYCOL
2CL-1Ligand/IonCHLORIDE ION
3GOL14Ligand/IonGLYCEROL
4MN-1Ligand/IonMANGANESE (II) ION
5PO44Ligand/IonPHOSPHATE ION
6SO48Ligand/IonSULFATE ION
7TRP4Mod. Amino AcidTRYPTOPHAN

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:87 , HIS A:369 , GLU A:411 , ASP A:441BINDING SITE FOR RESIDUE MN A 463
02AC2SOFTWAREVAL A:111 , LYS A:123 , ALA A:192 , CYS A:231 , ASN A:237 , THR A:240 , HOH A:2697 , HOH A:2698 , HOH A:2699 , HOH A:9043BINDING SITE FOR RESIDUE TRP A 9004
03AC3SOFTWAREGLY A:282 , GLU A:283 , LYS A:306 , ARG A:337 , HIS A:369 , HOH A:9020 , HOH A:9022 , HOH A:9318BINDING SITE FOR RESIDUE PO4 A 464
04AC4SOFTWAREMET A:92 , ARG A:168 , ARG A:171 , HOH A:2665 , HOH A:9216 , PRO B:8BINDING SITE FOR RESIDUE SO4 A 465
05AC5SOFTWAREARG A:135 , SER A:136 , ALA A:137 , ARG A:284BINDING SITE FOR RESIDUE SO4 A 466
06AC6SOFTWAREGLN A:70 , VAL A:121 , GLU A:242 , HOH A:2696 , HOH A:2697 , HOH A:2699 , HOH A:9030BINDING SITE FOR RESIDUE GOL A 2647
07AC7SOFTWAREGLU A:63 , THR A:187 , ILE A:243 , HOH A:2662BINDING SITE FOR RESIDUE GOL A 467
08AC8SOFTWAREMET A:92 , VAL A:170 , ARG A:171 , ASN A:175 , ASN B:175BINDING SITE FOR RESIDUE CE1 A 1001
09AC9SOFTWAREGLY B:282 , GLU B:283 , LYS B:306 , ARG B:337 , HIS B:369 , HOH B:9036 , HOH B:9205BINDING SITE FOR RESIDUE PO4 B 463
10BC1SOFTWAREARG B:135 , SER B:136 , ALA B:137 , ARG B:284BINDING SITE FOR RESIDUE SO4 B 464
11BC2SOFTWAREARG B:23 , LEU B:26 , ARG B:49 , ARG B:256 , GOL B:470 , HOH B:2662 , HOH B:9288 , HOH B:9326BINDING SITE FOR RESIDUE SO4 B 465
12BC3SOFTWARECYS B:87 , HIS B:369 , GLU B:411 , ASP B:441BINDING SITE FOR RESIDUE MN B 466
13BC4SOFTWARELYS B:123 , ALA B:192 , LEU B:194 , CYS B:231 , ASN B:237 , LEU B:238 , THR B:240 , ALA B:241 , HOH B:2667 , HOH B:2671 , HOH B:9095 , HOH B:9240BINDING SITE FOR RESIDUE TRP B 9004
14BC5SOFTWAREGLN B:70 , VAL B:121 , VAL B:122 , GLU B:242 , HOH B:2667 , HOH B:2671 , HOH B:2683 , HOH B:9111BINDING SITE FOR RESIDUE GOL B 2647
15BC6SOFTWAREARG B:25 , GLN B:270 , HIS B:326 , HOH B:2666 , HOH B:9039BINDING SITE FOR RESIDUE GOL B 467
16BC7SOFTWARETHR A:24 , ASP A:27 , HOH A:9017 , ARG B:25 , VAL B:298 , HOH B:2652BINDING SITE FOR RESIDUE GOL B 468
17BC8SOFTWAREPRO B:17 , LEU B:18 , ARG B:23 , HOH B:9030 , HOH B:9073BINDING SITE FOR RESIDUE CL B 469
18BC9SOFTWARELEU B:15 , PRO B:16 , LEU B:18 , ARG B:23 , ARG B:260 , LEU B:261 , SO4 B:465BINDING SITE FOR RESIDUE GOL B 470
19CC1SOFTWARETHR B:187 , ILE B:243 , HIS B:277 , HOH B:9056BINDING SITE FOR RESIDUE GOL B 471

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:87 -A:440
2B:87 -B:440

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NUE)

(-) Sequences/Alignments

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:453
 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 d3nuea_ A: Probable DAHP synthetase AroG, phenylalanine-repressible                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..........hhhhhhhhhhhhh.........hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...............................hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhh...eeeeee..hhhhhhhheee....-....eee....eeeehhhhh...hhhhhhhhhh...eeeee....hhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhhhh.....eeee......ee----...eehhhhhhhhhhhhhhhhhhhh....eeeee.......--.......----.............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nue A  -1 GAMNWTVDIPIDQLPSLPPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMPVVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQTAEIYASHEALVLDYERAMLRLSDGD-GEPQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKVQATGHQVIWQCDPMHGNTH----GFKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVT--LGGAQDI----LAGRYETACDPRLNTQQSLELAFLVAEMLRD 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  |     |-   |   438       448       458    
                                                                                                                                                                                                                                                                                                    265 |                                                                                                       373  378                                     418  |   427  432                              
                                                                                                                                                                                                                                                                                                      267                                                                                                                                                       421                                         


Chain B from PDB  Type:PROTEIN  Length:443
 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 d3nueb_ B: Probable DAHP synthetase AroG, phenylalanine-repressible                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeee..........hhhhhhhhhhhhh.........hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...............................hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhh...eeeeee..hhhhhhhheee.........eee....eeee........hhhhhhhhhh...eeeee....hhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhhhh.....eeee......-------....hhhhhhhhhhhhhhhhhhhh....eeeee.......-------------......-......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nue B  -1 GAMNWTVDIPIDQLPSLPPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMPVVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQTAEIYASHEALVLDYERAMLRLSDGDDGEPQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKVQATGHQVIWQCDPMHGN-------FKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVT-------------LAGRYE-ACDPRLNTQQSLELAFLVAEMLRD 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  |      -|      388       398       408       418         -   |    |-|      448       458    
                                                                                                                                                                                                                                                                                                                                                                                                              371     379                                    418           432  437 |                       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  439
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

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.

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  AROG_MYCTU | O53512
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AROG_MYCTU | O53512: 2b7o 2w19 2w1a 2ypo 2ypp 2ypq 3kgf 3nud 3nv8 3pfp 3rzi 5ckv 5ckx 5e2l 5e40 5e4n 5e5g 5e7z 5ex4

(-) Related Entries Specified in the PDB File

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