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(-) Description

Title :  HOLO 1L-MYO-INOSITOL-1-PHOSPHATE SYNTHASE
 
Authors :  A. J. Stein, J. H. Geiger
Date :  12 Jul 01  (Deposition) - 10 Apr 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Rossmann Fold, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Stein, J. H. Geiger
The Crystal Structure And Mechanism Of 1-L-Myo-Inositol- 1-Phosphate Synthase
J. Biol. Chem. V. 277 9484 2002
PubMed-ID: 11779862  |  Reference-DOI: 10.1074/JBC.M109371200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MYO-INOSITOL-1-PHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 5.5.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:72 , GLY B:74 , GLY B:75 , ASN B:76 , ASN B:77 , ASP B:148 , ILE B:149 , SER B:184 , ASN B:194 , GLN B:195 , ASP B:196 , GLU B:197 , THR B:244 , ALA B:245 , ASN B:246 , THR B:247 , SER B:296 , PRO B:297 , ASP B:320 , LEU B:321 , LYS B:322 , SER B:323 , ALA B:442 , HOH B:702 , HOH B:834BINDING SITE FOR RESIDUE NAD B 610
2AC2SOFTWAREILE A:71 , GLY A:72 , GLY A:74 , GLY A:75 , ASN A:76 , ASN A:77 , ASP A:148 , ILE A:149 , SER A:184 , ASN A:194 , ASP A:196 , GLU A:197 , TRP A:243 , THR A:244 , ALA A:245 , ASN A:246 , THR A:247 , SER A:296 , LEU A:321 , LYS A:322 , SER A:323 , GLY A:409 , ASP A:438 , HOH A:613BINDING SITE FOR RESIDUE NAD A 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YJL153C1YJL153C.1X:135929-1343281602INO1_YEAST1-5335332A:11-533 (gaps)
B:10-533 (gaps)		523
524

(-) 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:466
 aligned with INO1_YEAST | P11986 from UniProtKB/Swiss-Prot  Length:533

    Alignment length:523
                                    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       470       480       490       500       510       520       530   
           INO1_YEAST    11 SVKVVTDKCTYKDNELLTKYSYENAVVTKTASGRFDVTPTVQDYVFKLDLKKPEKLGIMLIGLGGNNGSTLVASVLANKHNVEFQTKEGVKQPNYFGSMTQCSTLKLGIDAEGNDVYAPFNSLLPMVSPNDFVVSGWDINNADLYEAMQRSQVLEYDLQQRLKAKMSLVKPLPSIYYPDFIAANQDERANNCINLDEKGNVTTRGKWTHLQRIRRDIQNFKEENALDKVIVLWTANTERYVEVSPGVNDTMENLLQSIKNDHEEIAPSTIFAAASILEGVPYINGSPQNTFVPGLVQLAEHEGTFIAGDDLKSGQTKLKSVLAQFLVDAGIKPVSIASYNHLGNNDGYNLSAPKQFRSKEISKSSVIDDIIASNDILYNDKLGKKVDHCIVIKYMKPVGDSKVAMDEYYSELMLGGHNRISIHNVCEDSLLATPLIIDLLVMTEFCTRVSYKKVDPVKEDAGKFENFYPVLTFLSYWLKAPLTRPGFHPVNGLNKQRTALENFLRLLIGLPSQNELRFEERLL 533
               SCOP domains d1jkfa1 A:11-322,A:438-533 Myo-inositol 1-phosphate synthase                                                                                                                                                                                                                                                            d1jkfa2 A:323-437 Myo-inosito                                                         l 1-phosphate synthase       d1jkfa1 A:11-322,A:438-533 Myo-inositol 1-phosphate synthase                                     SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1jkfA03 A:322-438 Dihydrodipic                                                         olinate Reductase; domain 2   ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eee...eeeeeee..eeeeee.....eeeeee..eeeeeee......eeeeee...hhhhhhhhhhhhhhhh...eee..eee......hhhhhheeeee.......eeee........hhh.eeeeee.....hhhhhhhhhh..hhhhhhhhhhhhh.........hhh.eee.....................hhhhhhhhhhhhhhhhhhhh....eeeee...ee...........hhhhhhhhhhhh....hhhhhhhhhhhhh...eee.......hhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhhh..eeeeee....---------------------------------------------------------...eeeeeeeeee.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.eeeeee..........ee....hhhhhhh..............hhhhhhhhhhhhhhhhh........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:11-533 (gaps) UniProt: 1-533 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  Transcript 1
                 1jkf A  11 SVKVVTDKCTYKDNELLTKYSYENAVVTKTASGRFDVTPTVQDYVFKLDLKKPEKLGIMLIGLGGNNGSTLVASVLANKHNVEFQTKEGVKQPNYFGSMTQCSTLKLGIDAEGNDVYAPFNSLLPMVSPNDFVVSGWDINNADLYEAMQRSQVLEYDLQQRLKAKMSLVKPLPSIYYPDFIAANQDERANNCINLDEKGNVTTRGKWTHLQRIRRDIQNFKEENALDKVIVLWTANTERYVEVSPGVNDTMENLLQSIKNDHEEIAPSTIFAAASILEGVPYINGSPQNTFVPGLVQLAEHEGTFIAGDDLKSGQTKLKSVLAQFLVDAGIKPVSIASYNH---------------------------------------------------------GDSKVAMDEYYSELMLGGHNRISIHNVCEDSLLATPLIIDLLVMTEFCTRVSYKKVDPVKEDAGKFENFYPVLTFLSYWLKAPLTRPGFHPVNGLNKQRTALENFLRLLIGLPSQNELRFEERLL 533
                                    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|        -         -         -         -         -       410       420       430       440       450       460       470       480       490       500       510       520       530   
                                                                                                                                                                                                                                                                                                                                                                              351                                                       409                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:465
 aligned with INO1_YEAST | P11986 from UniProtKB/Swiss-Prot  Length:533

    Alignment length:524
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529    
           INO1_YEAST    10 TSVKVVTDKCTYKDNELLTKYSYENAVVTKTASGRFDVTPTVQDYVFKLDLKKPEKLGIMLIGLGGNNGSTLVASVLANKHNVEFQTKEGVKQPNYFGSMTQCSTLKLGIDAEGNDVYAPFNSLLPMVSPNDFVVSGWDINNADLYEAMQRSQVLEYDLQQRLKAKMSLVKPLPSIYYPDFIAANQDERANNCINLDEKGNVTTRGKWTHLQRIRRDIQNFKEENALDKVIVLWTANTERYVEVSPGVNDTMENLLQSIKNDHEEIAPSTIFAAASILEGVPYINGSPQNTFVPGLVQLAEHEGTFIAGDDLKSGQTKLKSVLAQFLVDAGIKPVSIASYNHLGNNDGYNLSAPKQFRSKEISKSSVIDDIIASNDILYNDKLGKKVDHCIVIKYMKPVGDSKVAMDEYYSELMLGGHNRISIHNVCEDSLLATPLIIDLLVMTEFCTRVSYKKVDPVKEDAGKFENFYPVLTFLSYWLKAPLTRPGFHPVNGLNKQRTALENFLRLLIGLPSQNELRFEERLL 533
               SCOP domains d1jkfb1 B:10-322,B:438-533 Myo-inositol 1-phosphate synthase                                                                                                                                                                                                                                                             d1jkfb2 B:323-437 Myo-inosito                                                           l 1-phosphate synthase     d1jkfb1 B:10-322,B:438-533 Myo-inositol 1-phosphate synthase                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1jkfB03 B:322-438 Dihydrodipic                                                           olinate Reductase; domain 2 ----------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------------------------NAD_binding_5-1jkfB01 B:66-515                                                                                                                                                                                                                                                                                                                                                                                                                                    ------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------NAD_binding_5-1jkfB02 B:66-515                                                                                                                                                                                                                                                                                                                                                                                                                                    ------------------ Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Inos-1-P_synth-1jkfB03 B:324                                                           -439                         ---------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Inos-1-P_synth-1jkfB04 B:324                                                           -439                         ---------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..eee....eee....eeeeee..eeee.......eeeeee..eeeeee.......eeeeee...hhhhhhhhhhhhhhhh...eee..eee......hhhhhheeeee.......eeee........hhh.eeeeee.....hhhhhhhhh...hhhhhhhhhhhhhh........hhhhh.......................hhhhhhhhhhhhhhhhhhhhh...eeeee..................hhhhhhhhh.....hhhhhhhhhhhh....eee.......hhhhhhhhhhhhh.ee.......hhhhhhhhhhhhhh...eeeeeee...-----------------------------------------------------------.eeeeeeeeee.hhh.eeeeeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeee..........ee......hhhhh..............hhhhhhhhhhhhhhhh.........hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:10-533 (gaps) UniProt: 1-533 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   Transcript 1
                 1jkf B  10 TSVKVVTDKCTYKDNELLTKYSYENAVVTKTASGRFDVTPTVQDYVFKLDLKKPEKLGIMLIGLGGNNGSTLVASVLANKHNVEFQTKEGVKQPNYFGSMTQCSTLKLGIDAEGNDVYAPFNSLLPMVSPNDFVVSGWDINNADLYEAMQRSQVLEYDLQQRLKAKMSLVKPLPSIYYPDFIAANQDERANNCINLDEKGNVTTRGKWTHLQRIRRDIQNFKEENALDKVIVLWTANTERYVEVSPGVNDTMENLLQSIKNDHEEIAPSTIFAAASILEGVPYINGSPQNTFVPGLVQLAEHEGTFIAGDDLKSGQTKLKSVLAQFLVDAGIKPVSIASYNH-----------------------------------------------------------SKVAMDEYYSELMLGGHNRISIHNVCEDSLLATPLIIDLLVMTEFCTRVSYKKVDPVKEDAGKFENFYPVLTFLSYWLKAPLTRPGFHPVNGLNKQRTALENFLRLLIGLPSQNELRFEERLL 533
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349 |       -         -         -         -         -         - |     419       429       439       449       459       469       479       489       499       509       519       529    
                                                                                                                                                                                                                                                                                                                                                                               351                                                         411
   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, 4)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: Inos-1-P_synth] (10)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (INO1_YEAST | P11986)
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:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1jkf
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  5.5.1.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        INO1_YEAST | P11986: 1jki 1la2 1p1f 1p1h 1p1i 1p1j 1p1k 1rm0

(-) Related Entries Specified in the PDB File

1jki MYO-INOSITOL-1-PHOSPHATE SYNTHASE COMPLEXED WITH AN INHIBITOR, 2-DEOXY-GLUCITOL-6-PHOSPHATE