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(-) Description

Title :  MYO-INOSITOL 1-PHOSPHATE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH NAD AND ZINC.
 
Authors :  R. A. Norman, J. Murray-Rust, N. Q. Mcdonald, Tb Structural Genomics Consortium (Tbsgc)
Date :  10 Dec 01  (Deposition) - 12 Mar 02  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Isomerase, Oxidoreductase, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tb, Tbsgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. A. Norman, M. S. B. Mcalister, J. Murray-Rust, F. Movahedzadeh, N. G. Stoker, N. Q. Mcdonald
Crystal Structure Of Inositol 1-Phosphate Synthase From Mycobacterium Tuberculosis, A Key Enzyme In Phosphatidylinositol Synthesis
Structure V. 10 393 2002
PubMed-ID: 12005437  |  Reference-DOI: 10.1016/S0969-2126(02)00718-9

(-) Compounds

Molecule 1 - INOSITOL-3-PHOSPHATE SYNTHASE
    Chains: A
    EC Number: 5.5.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Taxid: 562
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: IPS, MYO-INOSITOL-1-PHOSPHATE SYNTHASE, MI-1-P SYNTHASE, MIP SYNTHASE, HYPOTHETICAL 40.1 KDA PROTEIN RV0046C

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION
2NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CAC4Ligand/IonCACODYLATE ION
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:26 , SER A:311 , NAD A:1000 , HOH A:2170BINDING SITE FOR RESIDUE ZN A1200
2AC2SOFTWARETHR A:43 , SER A:44 , HIS A:51 , HOH A:2015 , HOH A:2019BINDING SITE FOR RESIDUE CAC A1500
3AC3SOFTWAREGLY A:22 , VAL A:23 , GLY A:24 , ASN A:25 , CYS A:26 , PHE A:68 , ASP A:69 , VAL A:70 , LYS A:74 , PRO A:107 , THR A:108 , GLY A:111 , ILE A:112 , TYR A:116 , TYR A:145 , LEU A:146 , PRO A:147 , VAL A:148 , TYR A:157 , ALA A:171 , LEU A:172 , ASP A:197 , ILE A:198 , MET A:234 , ASP A:235 , ASP A:310 , SER A:311 , SER A:314 , ZN A:1200 , HOH A:2001 , HOH A:2002 , HOH A:2035 , HOH A:2168 , HOH A:2169BINDING SITE FOR RESIDUE NAD A1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GR0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GR0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GR0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GR0)

(-) Exons   (0, 0)

(no "Exon" information available for 1GR0)

(-) 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:328
 aligned with INO1_MYCTO | P9WKI0 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:354
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363    
           INO1_MYCTO    14 TEVRVAIVGVGNCASSLVQGVEYYYNADDTSTVPGLMHVRFGPYHVRDVKFVAAFDVDAKKVGFDLSDAIFASENNTIKIADVAPTNVIVQRGPTLDGIGKYYADTIELSDAEPVDVVQALKEAKVDVLVSYLPVGSEEADKFYAQCAIDAGVAFVNALPVFIASDPVWAKKFTDAGVPIVGDDIKSQVGATITHRVLAKLFEDRGVQLDRTMQLNVGGNMDFLNMLERERLESKKISKTQAVTSNLKREFKTKDVHIGPSDHVGWLDDRKWAYVRLEGRAFGDVPLNLEYKLEVWDSPNSAGVIIDAVRAAKIAKDRGIGGPVIPASAYLMKSPPEQLPDDIARAQLEEFIIG 367
               SCOP domains d1gr0a1 A:14-200,A:312-367 Myo-inositol 1-phosphate synthase                                                                                                                               d1gr0a2 A:201-311 Myo-inositol 1-phosphat                          e synthase                                  d1gr0a1 A:14-200,A:312-367                               SCOP domains
               CATH domains 1gr0A01 A:14-201,A:312-366 NAD(P)-binding Rossmann-like Domain                                                                                                                              1gr0A02 A:202-311 Dihydrodipicolinate Re                          ductase; domain 2                           1gr0A01 A:14-201,A:312-366                             - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh...............ee..ee...eeeeeeee........hhhhhh....................ee.......hhhhhh..........hhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh.eeee........hhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhh..eeeeeeeeeee.hhhhhhhhh--------------------------.ee..eeee......eeeeeeeeeeee...eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhh.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gr0 A  14 TEVRVAIVGVGNCASSLVQGVEYYYNADDTSTVPGLMHVRFGPYHVRDVKFVAAFDVDAKKVGFDLSDAIFASENNTIKIADVAPTNVIVQRGPTLDGIGKYYADTIELSDAEPVDVVQALKEAKVDVLVSYLPVGSEEADKFYAQCAIDAGVAFVNALPVFIASDPVWAKKFTDARVPIVGDDIKSQVGATITHRVLAKLFEDRGVQLDRTMQLNVGGNMDFLNMLE--------------------------DVHIGPSDHVGWLDDRKWAYVRLEGRAFGDVPLNLEYKLEVWDSPNSAGVIIDAVRAAKIAKDRGIGGPVIPASAYLMKSPPEQLPDDIARAQLEEFIIG 367
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       | -         -         -    |  273       283       293       303       313       323       333       343       353       363    
                                                                                                                                                                                                                                                             241                        268                                                                                                   


Chain A from PDB  Type:PROTEIN  Length:328
 aligned with INO1_MYCTU | P9WKI1 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:354
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363    
           INO1_MYCTU    14 TEVRVAIVGVGNCASSLVQGVEYYYNADDTSTVPGLMHVRFGPYHVRDVKFVAAFDVDAKKVGFDLSDAIFASENNTIKIADVAPTNVIVQRGPTLDGIGKYYADTIELSDAEPVDVVQALKEAKVDVLVSYLPVGSEEADKFYAQCAIDAGVAFVNALPVFIASDPVWAKKFTDARVPIVGDDIKSQVGATITHRVLAKLFEDRGVQLDRTMQLNVGGNMDFLNMLERERLESKKISKTQAVTSNLKREFKTKDVHIGPSDHVGWLDDRKWAYVRLEGRAFGDVPLNLEYKLEVWDSPNSAGVIIDAVRAAKIAKDRGIGGPVIPASAYLMKSPPEQLPDDIARAQLEEFIIG 367
               SCOP domains d1gr0a1 A:14-200,A:312-367 Myo-inositol 1-phosphate synthase                                                                                                                               d1gr0a2 A:201-311 Myo-inositol 1-phosphat                          e synthase                                  d1gr0a1 A:14-200,A:312-367                               SCOP domains
               CATH domains 1gr0A01 A:14-201,A:312-366 NAD(P)-binding Rossmann-like Domain                                                                                                                              1gr0A02 A:202-311 Dihydrodipicolinate Re                          ductase; domain 2                           1gr0A01 A:14-201,A:312-366                             - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh...............ee..ee...eeeeeeee........hhhhhh....................ee.......hhhhhh..........hhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh.eeee........hhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhh..eeeeeeeeeee.hhhhhhhhh--------------------------.ee..eeee......eeeeeeeeeeee...eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhh.......hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gr0 A  14 TEVRVAIVGVGNCASSLVQGVEYYYNADDTSTVPGLMHVRFGPYHVRDVKFVAAFDVDAKKVGFDLSDAIFASENNTIKIADVAPTNVIVQRGPTLDGIGKYYADTIELSDAEPVDVVQALKEAKVDVLVSYLPVGSEEADKFYAQCAIDAGVAFVNALPVFIASDPVWAKKFTDARVPIVGDDIKSQVGATITHRVLAKLFEDRGVQLDRTMQLNVGGNMDFLNMLE--------------------------DVHIGPSDHVGWLDDRKWAYVRLEGRAFGDVPLNLEYKLEVWDSPNSAGVIIDAVRAAKIAKDRGIGGPVIPASAYLMKSPPEQLPDDIARAQLEEFIIG 367
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       | -         -         -    |  273       283       293       303       313       323       333       343       353       363    
                                                                                                                                                                                                                                                             241                        268
   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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GR0)

(-) Gene Ontology  (8, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (INO1_MYCTU | P9WKI1)
molecular function
    GO:0004512    inositol-3-phosphate synthase activity    Catalysis of the reaction: D-glucose 6-phosphate = 1D-myo-inositol 3-phosphate. This reaction requires NAD, which dehydrogenates the CHOH group to CO at C-5 of the glucose 6-phosphate, making C-6 into an active methylene, able to condense with the aldehyde at C-1. Finally, the enzyme-bound NADH reconverts C-5 into the CHOH form.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006021    inositol biosynthetic process    The chemical reactions and pathways resulting in the formation of inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.
    GO:0010125    mycothiol biosynthetic process    The chemical reactions and pathways resulting in the formation of mycothiol, which consists of N-acetyl-L-cysteine linked to a pseudodisaccharide, D-glucosamine and myo-inositol. Mycothiol is produced in actinomycetes like mycobacteria and serves similar functions to glutathione.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0008654    phospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A   (INO1_MYCTO | P9WKI0)
molecular function
    GO:0004512    inositol-3-phosphate synthase activity    Catalysis of the reaction: D-glucose 6-phosphate = 1D-myo-inositol 3-phosphate. This reaction requires NAD, which dehydrogenates the CHOH group to CO at C-5 of the glucose 6-phosphate, making C-6 into an active methylene, able to condense with the aldehyde at C-1. Finally, the enzyme-bound NADH reconverts C-5 into the CHOH form.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0006021    inositol biosynthetic process    The chemical reactions and pathways resulting in the formation of inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.
    GO:0008654    phospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.

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  1gr0
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