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(-) Description

Title :  THE STRUCTURE OF 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS COCRYSTALLIZED AND COMPLEXED WITH PHENYLALANINE AND TRYPTOPHAN
 
Authors :  W. Jiao, G. B. Jameson, R. D. Hutton, E. J. Parker
Date :  11 May 11  (Deposition) - 25 Jan 12  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Dah7P Synthase, Shikimate Pathway, Aromatic Biosynthesis, Evolutionary Relationships, Transferase, Phe+Trp-Bound, Augmented Tim-Barrel Structure, Structural Genomics, Mycobacterium Tuberculosis Structural Proteomics Project, Xmtb, Tim Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Jiao, R. D. Hutton, P. J. Cross, G. B. Jameson, E. J. Parker
Dynamic Cross-Talk Among Remote Binding Sites: The Molecula Basis For Unusual Synergistic Allostery.
J. Mol. Biol. V. 415 716 2012
PubMed-ID: 22154807  |  Reference-DOI: 10.1016/J.JMB.2011.11.037

(-) 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
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AROG, RV2178C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    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, 22)

Asymmetric Unit (7, 22)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL8Ligand/IonGLYCEROL
3MN2Ligand/IonMANGANESE (II) ION
4PHE2Mod. Amino AcidPHENYLALANINE
5PO42Ligand/IonPHOSPHATE ION
6SO44Ligand/IonSULFATE ION
7TRP2Mod. Amino AcidTRYPTOPHAN
Biological Unit 1 (5, 36)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL16Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4PHE4Mod. Amino AcidPHENYLALANINE
5PO44Ligand/IonPHOSPHATE ION
6SO48Ligand/IonSULFATE ION
7TRP4Mod. Amino AcidTRYPTOPHAN

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:87 , HIS A:369 , GLU A:411 , ASP A:441 , HOH A:567BINDING SITE FOR RESIDUE MN A 463
02AC2SOFTWAREPHE A:91 , ARG A:171 , ALA A:174 , ASN A:175 , HOH A:487 , HOH A:599 , VAL B:5BINDING SITE FOR RESIDUE PHE A 464
03AC3SOFTWARELEU A:107 , VAL A:111 , LYS A:123 , ALA A:192 , LEU A:194 , CYS A:231 , ASN A:237 , LEU A:238 , THR A:240 , ALA A:241 , GOL A:469 , HOH A:496 , HOH A:514 , HOH A:633BINDING SITE FOR RESIDUE TRP A 465
04AC4SOFTWAREGLY A:282 , GLU A:283 , LYS A:306 , ARG A:337 , HIS A:369BINDING SITE FOR RESIDUE PO4 A 466
05AC5SOFTWARETHR A:39 , ARG A:145 , ARG A:148 , HIS A:164 , HOH A:528BINDING SITE FOR RESIDUE SO4 A 467
06AC6SOFTWAREGLU A:63 , THR A:187 , GLU A:242 , ILE A:243 , TYR A:244 , HOH A:664BINDING SITE FOR RESIDUE GOL A 468
07AC7SOFTWAREGLN A:70 , VAL A:121 , VAL A:122 , LYS A:123 , GLU A:242 , TRP A:465 , HOH A:496 , HOH A:592BINDING SITE FOR RESIDUE GOL A 469
08AC8SOFTWAREGLN A:36BINDING SITE FOR RESIDUE CL A 470
09AC9SOFTWAREARG A:135 , SER A:136 , ALA A:137 , ARG A:284BINDING SITE FOR RESIDUE GOL A 471
10BC1SOFTWARECYS B:87 , HIS B:369 , GLU B:411 , ASP B:441 , HOH B:533BINDING SITE FOR RESIDUE MN B 463
11BC2SOFTWARELEU B:30 , ASP B:253 , ARG B:256BINDING SITE FOR RESIDUE GOL B 464
12BC3SOFTWAREVAL A:55 , TYR A:173 , HOH A:616 , PHE B:91 , ARG B:171 , ALA B:174 , ASN B:175 , HOH B:598BINDING SITE FOR RESIDUE PHE B 465
13BC4SOFTWAREVAL B:111 , LYS B:123 , ALA B:192 , LEU B:194 , ASN B:237 , LEU B:238 , THR B:240 , ALA B:241 , HOH B:510 , HOH B:560 , HOH B:584 , HOH B:694BINDING SITE FOR RESIDUE TRP B 466
14BC5SOFTWAREGLY B:282 , GLU B:283 , LYS B:306 , ARG B:337 , HOH B:593 , HOH B:635 , HOH B:651BINDING SITE FOR RESIDUE PO4 B 467
15BC6SOFTWAREARG B:135 , SER B:136 , ALA B:137 , ARG B:284 , HOH B:727BINDING SITE FOR RESIDUE SO4 B 468
16BC7SOFTWAREPRO B:17 , LEU B:18 , ARG B:23 , LEU B:144 , ASP B:158 , ALA B:159 , HOH B:480 , HOH B:634BINDING SITE FOR RESIDUE SO4 B 469
17BC8SOFTWAREARG B:23 , ARG B:256 , HOH B:562 , HOH B:606BINDING SITE FOR RESIDUE SO4 B 470
18BC9SOFTWAREARG A:23 , THR A:24 , ASP A:27 , GLN B:297 , ARG B:322 , HOH B:487 , HOH B:537BINDING SITE FOR RESIDUE GOL B 472
19CC1SOFTWAREMET B:180 , THR B:187 , GLU B:242 , ILE B:243 , HIS B:277BINDING SITE FOR RESIDUE GOL B 473
20CC2SOFTWAREMET B:92 , ASP B:93 , PHE B:155 , GLU B:437 , HOH B:540BINDING SITE FOR RESIDUE GOL B 474
21CC3SOFTWAREGLN B:70 , PRO B:120 , VAL B:121 , GLU B:242 , HOH B:510 , HOH B:511 , HOH B:535 , HOH B:584BINDING SITE FOR RESIDUE GOL B 475

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RZI)

(-) 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:461
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461 
           AROG_MYCTU     2 NWTVDIPIDQLPSLPPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMPVVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQTAEIYASHEALVLDYERAMLRLSDGDDGEPQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKVQATGHQVIWQCDPMHGNTHESSTGFKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVTECLGGAQDISETDLAGRYETACDPRLNTQQSLELAFLVAEMLRD 462
               SCOP domains d3rzia_ A:     automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...----...hhhhhhhhhhhhh.........hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...............................hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhh....eeeee..hhhhhhhheee...----..eee....eeee........hhhhhhhhhh...eeeee....hhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhhhhh....eeee......eee.....eeehhhhhhhhhhhhhhhhhhhh....eeeee..................hhhhh..........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rzi A   2 NWTVDIPIDQ----PPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMPVVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQTAEIYASHEALVLDYERAMLRLSDG----PQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKVQATGHQVIWQCDPMHGNTHESSTGFKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVTECLGGAQDISETDLAGRYETACDPRLNTQQSLELAFLVAEMLRD 462
                                    11    |   21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  |    271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461 
                                    11   16                                                                                                                                                                                                                                                     264  269                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:457
 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 d3rzib_ B     : automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...-----....hhhhhhhhhhhhhh........hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...............................hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhh...eeeeee..hhhhhhhheee.........eee....eeeehhhhh...hhhhhhhhhh...eeeee....hhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhhhh.....eeee......eee.....eeehhhhhhhhhhhhhhhhhhhh....eeeee..................hhhhh..........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rzi B   1 MNWTVDIPI-----LPPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMPVVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQTAEIYASHEALVLDYERAMLRLSDGDDGEPQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKVQATGHQVIWQCDPMHGNTHESSTGFKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVTECLGGAQDISETDLAGRYETACDPRLNTQQSLELAFLVAEMLRD 462
                                    |-    |   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  
                                    9    15
   Legend:   → Mismatch (orange background)
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  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 3RZI)

(-) Pfam Domains  (0, 0)

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

(-) 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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  3rzi
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  AROG_MYCTU | O53512
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  2.5.1.54
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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 3nue 3nv8 3pfp 5ckv 5ckx 5e2l 5e40 5e4n 5e5g 5e7z 5ex4

(-) Related Entries Specified in the PDB File

3kgf THE SAME PROTEIN (SOAKED WITH 2 MM EACH OF PHE+TRP)
3nud THE SAME PROTEIN (WITH PHE BOUND IN PHE AND TRP SITES)
3nue THE SAME PROTEIN (WITH TRP BOUND IN ONLY THE TRP SITE)
3nv8 THE SAME PROTEIN (THESIT-FREE WITH PEP BOUND)