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(-) Description

Title :  CRYSTAL STRUCTURE OF APO 1L-MYO-INOSITOL 1-PHOSPHATE SYNTHASE
 
Authors :  X. Jin, J. H. Geiger
Date :  12 Apr 03  (Deposition) - 08 Jul 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Apo, Enzyme, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Jin, J. H. Geiger
Structures Of Nad(+)- And Nadh-Bound 1-L-Myo-Inositol 1-Phosphate Synthase.
Acta Crystallogr. , Sect. D V. 59 1154 2003
PubMed-ID: 12832758  |  Reference-DOI: 10.1107/S0907444903008205

(-) Compounds

Molecule 1 - INOSITOL-3-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
    Synonym: 1L-MYO-INOSITOL 1-PHOSPHATE SYNTHASE, MYO-INOSITOL-1- PHOSPHATE SYNTHASE, MI-1-P SYNTHASE, IPS

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1P1F)

(-) Sites  (0, 0)

(no "Site" information available for 1P1F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P1F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P1F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P1F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P1F)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YJL153C1YJL153C.1X:135929-1343281602INO1_YEAST1-5335332A:9-533 (gaps)
B:9-533 (gaps)		525
525

(-) 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:501
 aligned with INO1_YEAST | P11986 from UniProtKB/Swiss-Prot  Length:533

    Alignment length:525
                                    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       468       478       488       498       508       518       528     
           INO1_YEAST     9 ITSVKVVTDKCTYKDNELLTKYSYENAVVTKTASGRFDVTPTVQDYVFKLDLKKPEKLGIMLIGLGGNNGSTLVASVLANKHNVEFQTKEGVKQPNYFGSMTQCSTLKLGIDAEGNDVYAPFNSLLPMVSPNDFVVSGWDINNADLYEAMQRSQVLEYDLQQRLKAKMSLVKPLPSIYYPDFIAANQDERANNCINLDEKGNVTTRGKWTHLQRIRRDIQNFKEENALDKVIVLWTANTERYVEVSPGVNDTMENLLQSIKNDHEEIAPSTIFAAASILEGVPYINGSPQNTFVPGLVQLAEHEGTFIAGDDLKSGQTKLKSVLAQFLVDAGIKPVSIASYNHLGNNDGYNLSAPKQFRSKEISKSSVIDDIIASNDILYNDKLGKKVDHCIVIKYMKPVGDSKVAMDEYYSELMLGGHNRISIHNVCEDSLLATPLIIDLLVMTEFCTRVSYKKVDPVKEDAGKFENFYPVLTFLSYWLKAPLTRPGFHPVNGLNKQRTALENFLRLLIGLPSQNELRFEERLL 533
               SCOP domains d1p1fa1 A:9-322,A:438-533 Myo-inositol 1-phosphate synthase                                                                                                                                                                                                                                                               d1p1fa2 A:323-437 Myo-inosito                        l 1-phosphate synthase                                        d1p1fa1 A:9-322,A:438-533 Myo-inositol 1-phosphate synthase                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....eee...eeeeeeeeeeeeee.....eeeeeeeeeeeeeeee......eeeeee...hhhhhhhhhhhhhhhh.................hhhhhheeeee.......eeee.hhh....hhh.eeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhh........hhhhh.......................hhhhhhhhhhhhhhhhhhhhh..eeeeee................hhhhhhhhhhh.....hhhhhhhhhhhhh...eee.......hhhhhhhhhhhh..ee.....hhhhhhhhhhhhhhhh...eeeeeeeeee------------------------.hhhhhh.................eee..........eeeeeeeee.hhh.eeeeeeeee.hhhhhhhhhhhhhhhhhhhhh.eee.ee..........ee....hhhhhhhh.............hhhhhhhhhhhhhhhhh........hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:9-533 (gaps) UniProt: 1-533 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 1p1f A   9 ITSVKVVTDKCTYKDNELLTKYSYENAVVTKTASGRFDVTPTVQDYVFKLDLKKPEKLGIMLIGLGGNNGSTLVASVLANKHNVEFQTKEGVKQPNYFGSMTQCSTLKLGIDAEGNDVYAPFNSLLPMVSPNDFVVSGWDINNADLYEAMQRSQVLEYDLQQRLKAKMSLVKPLPSIYYPDFIAANQDERANNCINLDEKGNVTTRGKWTHLQRIRRDIQNFKEENALDKVIVLWTANTERYVEVSPGVNDTMENLLQSIKNDHEEIAPSTIFAAASILEGVPYINGSPQNTFVPGLVQLAEHEGTFIAGDDLKSGQTKLKSVLAQFLVDAGIKPVSIASYNH------------------------VIDDIIASNDILYNDKLGKKVDHCIVIKYMKPVGDSKVAMDEYYSELMLGGHNRISIHNVCEDSLLATPLIIDLLVMTEFCTRVSYKKVDPVKEDAGKFENFYPVLTFLSYWLKAPLTRPGFHPVNGLNKQRTALENFLRLLIGLPSQNELRFEERLL 533
                                    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  |      -         -       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528     
                                                                                                                                                                                                                                                                                                                                                                                351                      376                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:496
 aligned with INO1_YEAST | P11986 from UniProtKB/Swiss-Prot  Length:533

    Alignment length:525
                                    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       468       478       488       498       508       518       528     
           INO1_YEAST     9 ITSVKVVTDKCTYKDNELLTKYSYENAVVTKTASGRFDVTPTVQDYVFKLDLKKPEKLGIMLIGLGGNNGSTLVASVLANKHNVEFQTKEGVKQPNYFGSMTQCSTLKLGIDAEGNDVYAPFNSLLPMVSPNDFVVSGWDINNADLYEAMQRSQVLEYDLQQRLKAKMSLVKPLPSIYYPDFIAANQDERANNCINLDEKGNVTTRGKWTHLQRIRRDIQNFKEENALDKVIVLWTANTERYVEVSPGVNDTMENLLQSIKNDHEEIAPSTIFAAASILEGVPYINGSPQNTFVPGLVQLAEHEGTFIAGDDLKSGQTKLKSVLAQFLVDAGIKPVSIASYNHLGNNDGYNLSAPKQFRSKEISKSSVIDDIIASNDILYNDKLGKKVDHCIVIKYMKPVGDSKVAMDEYYSELMLGGHNRISIHNVCEDSLLATPLIIDLLVMTEFCTRVSYKKVDPVKEDAGKFENFYPVLTFLSYWLKAPLTRPGFHPVNGLNKQRTALENFLRLLIGLPSQNELRFEERLL 533
               SCOP domains d1p1fb1 B:9-322,B:438-533 Myo-inositol 1-phosphate synthase                                                                                                                                                                                                                                                               d1p1fb2 B:323-437 Myo-inositol                        1-phosphate synthase                                         d1p1fb1 B:9-322,B:438-533 Myo      -inositol 1-phosphate synthase                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------NAD_binding_5-1p1fB01 B:66-515                                                                                                                                                                                                                                                                                                                                                                                                                                    ------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------NAD_binding_5-1p1fB02 B:66-515                                                                                                                                                                                                                                                                                                                                                                                                                                    ------------------ Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Inos-1-P_synth-1p1fB03 B:324-                       439                                                             ---------------------------      ------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Inos-1-P_synth-1p1fB04 B:324-                       439                                                             ---------------------------      ------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..eeee....ee......eeeeee..eeeeee...eeeeee..eeeeeee.......eeeeee...hhhhhhhhhhhhhhhh.................hhhhhheeeeee.....eeeee.hhh....hhh.eeee.......hhhhhhhhhh..hhhhhhhhhhhhh.........hhhhh.............ee..eee...hhhhhhhhhhhhhhhhhhhhh...eeeee................hhhhhhhhhhhh....hhhhhhhhhhhh....eee.......hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.eeeeeeeeeee-----------------------.hhhhhhhh............eeeeeeee.......eeeeeeeeee.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhheeee....------...........hhhhh..............hhhhhhhhhhhhhhhh........hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:9-533 (gaps) UniProt: 1-533 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 1p1f B   9 ITSVKVVTDKCTYKDNELLTKYSYENAVVTKTASGRFDVTPTVQDYVFKLDLKKPEKLGIMLIGLGGNNGSTLVASVLANKHNVEFQTKEGVKQPNYFGSMTQCSTLKLGIDAEGNDVYAPFNSLLPMVSPNDFVVSGWDINNADLYEAMQRSQVLEYDLQQRLKAKMSLVKPLPSIYYPDFIAANQDERANNCINLDEKGNVTTRGKWTHLQRIRRDIQNFKEENALDKVIVLWTANTERYVEVSPGVNDTMENLLQSIKNDHEEIAPSTIFAAASILEGVPYINGSPQNTFVPGLVQLAEHEGTFIAGDDLKSGQTKLKSVLAQFLVDAGIKPVSIASYNHL-----------------------VIDDIIASNDILYNDKLGKKVDHCIVIKYMKPVGDSKVAMDEYYSELMLGGHNRISIHNVCEDSLLATPLIIDLLVMTEFCTRVSYKKVDP------KFENFYPVLTFLSYWLKAPLTRPGFHPVNGLNKQRTALENFLRLLIGLPSQNELRFEERLL 533
                                    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   |     -         -       378       388       398       408       418       428       438       448       458       | -    |  478       488       498       508       518       528     
                                                                                                                                                                                                                                                                                                                                                                                 352                     376                                                                                       466    473
   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  (0, 0)

(no "CATH Domain" information available for 1P1F)

(-) 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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  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: 1jkf 1jki 1la2 1p1h 1p1i 1p1j 1p1k 1rm0

(-) Related Entries Specified in the PDB File

1p1h CRYSTAL STRUCTURE OF 1L-MYO-INOSITOL 1-PHOSPHATE SYNTHASE
1p1i CRYSTAL STRUCTURE OF THE NAD+-BOUND 1L-MYO-INOSITOL 1- PHOSPHATE SYNTHASE
1p1j CRYSTAL STRUCTURE OF THE 1L-MYO-INOSITOL 1-PHOSPHATE SYNTHASE COMPLEXED WITH NADH
1p1k CRYSTAL STRUCTURE OF THE 1L-MYO-INOSITOL 1-PHOSPHATE SYNTHASE COMPLEXED WITH NADH AND EDTA