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(-) Description

Title :  L-MYO-INOSITOL 1-PHOSPHATE SYNTHASE FROM ARCHAEOGLOBUS FULGIDUS MUTANT K367A
 
Authors :  K. Neelon, M. F. Roberts, B. Stec
Date :  26 Feb 11  (Deposition) - 11 Jan 12  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  L-Myo-Inositol 1-Phosphate Synthase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Neelon, M. F. Roberts, B. Stec
Atomic Crowding Drives The Catalysis Of Myo-Inositol Phosphate Synthase, As Deduced From A Crystal Structure Of Trapped Catalytic Intermediate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MYO-INOSITOL-1-PHOSPHATE SYNTHASE (INO1)
    Chains: A
    EC Number: 5.5.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AF1794, AF_1794
    Mutation: YES
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: MIPS

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 10)

Asymmetric Unit (6, 10)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2NA1Ligand/IonSODIUM ION
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5PO41Ligand/IonPHOSPHATE ION
6SO42Ligand/IonSULFATE ION
Biological Unit 1 (5, 36)
No.NameCountTypeFull Name
1GOL16Ligand/IonGLYCEROL
2NA-1Ligand/IonSODIUM ION
3NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4PG44Ligand/IonTETRAETHYLENE GLYCOL
5PO44Ligand/IonPHOSPHATE ION
6SO48Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:228 , GLY A:229 , GLU A:230 , THR A:231 , LYS A:274 , LYS A:278 , LYS A:306 , GOL A:397 , HOH A:445BINDING SITE FOR RESIDUE PO4 A 393
02AC2SOFTWAREARG A:175 , LYS A:176 , GLU A:177BINDING SITE FOR RESIDUE SO4 A 394
03AC3SOFTWARELYS A:360 , THR A:372 , ASN A:373BINDING SITE FOR RESIDUE SO4 A 395
04AC4SOFTWAREGLY A:7 , TYR A:9 , GLY A:10 , ILE A:11 , VAL A:12 , GLU A:57 , ARG A:59 , THR A:99 , ALA A:100 , CYS A:103 , LEU A:110 , VAL A:147 , ALA A:148 , SER A:149 , THR A:150 , ALA A:181 , TYR A:185 , PHE A:199 , THR A:200 , ASP A:225 , GLY A:226 , THR A:228 , TYR A:260 , ASP A:261 , LYS A:274 , ASP A:332 , ALA A:336 , GOL A:397 , HOH A:421 , HOH A:423 , HOH A:426 , HOH A:437 , HOH A:441 , HOH A:501BINDING SITE FOR RESIDUE NAD A 396
05AC5SOFTWAREASP A:261 , LYS A:274 , LYS A:278 , LYS A:306 , ASP A:332 , PO4 A:393 , NAD A:396BINDING SITE FOR RESIDUE GOL A 397
06AC6SOFTWARELYS A:263 , TYR A:298 , PRO A:300 , HOH A:574BINDING SITE FOR RESIDUE GOL A 398
07AC7SOFTWAREASN A:305 , LEU A:321 , LYS A:323 , ASP A:329 , HOH A:414 , HOH A:432 , HOH A:603BINDING SITE FOR RESIDUE GOL A 403
08AC8SOFTWAREASN A:75 , LEU A:302 , VAL A:303 , ASN A:305 , ILE A:331 , HOH A:414BINDING SITE FOR RESIDUE GOL A 404
09AC9SOFTWAREGLU A:131 , GLU A:132 , LYS A:135 , SER A:289 , PRO A:290 , SER A:292BINDING SITE FOR RESIDUE PG4 A 399
10BC1SOFTWARETYR A:325 , ASP A:329BINDING SITE FOR RESIDUE NA A 410

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:223 -Asn A:224

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QVX)

(-) 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:392
 aligned with O28480_ARCFU | O28480 from UniProtKB/TrEMBL  Length:392

    Alignment length:392
                                    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  
         O28480_ARCFU     1 MKVWLVGAYGIVSTTAMVGARAIERGIAPKIGLVSELPHFEGIEKYAPFSFEFGGHEIRLLSNAYEAAKEHWELNRHFDREILEAVKSDLEGIVARKGTALNCGSGIKELGDIKTLEGEGLSLAEMVSRIEEDIKSFADDETVVINVASTEPLPNYSEEYHGSLEGFERMIDEDRKEYASASMLYAYAALKLGLPYANFTPSPGSAIPALKELAEKKGVPHAGNDGKTGETLVKTTLAPMFAYRNMEVVGWMSYNILGDYDGKVLSARDNKESKVLSKDKVLEKMLGYSPYSITEIQYFPSLVDNKTAFDFVHFKGFLGKLMKFYFIWDAIDAIVAAPLILDIARFLLFAKKKGVKGVVKEMAFFFKSPMDTNVINTHEQFVVLKEWYSNLK 392
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhh...ee......hhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhh...eeeeeeeee.hhh.eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...ee.hhhhhhh.........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qvx A   1 MKVWLVGAYGIVSTTAMVGARAIERGIAPKIGLVSELPHFEGIEKYAPFSFEFGGHEIRLLSNAYEAAKEHWELNRHFDREILEAVKSDLEGIVARKGTALNCGSGIKELGDIKTLEGEGLSLAEMVSRIEEDIKSFADDETVVINVASTEPLPNYSEEYHGSLEGFERMIDEDRKEYASASMLYAYAALKLGLPYANFTPSPGSAIPALKELAEKKGVPHAGNDGKTGETLVKTTLAPMFAYRNMEVVGWMSYNILGDYDGKVLSARDNKESKVLSKDKVLEKMLGYSPYSITEIQYFPSLVDNKTAFDFVHFKGFLGKLMKFYFIWDAIDAIVAAPLILDIARFLLFAKKKGVKGVVKEMAFFFASPMDTNVINTHEQFVVLKEWYSNLK 392
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 3QVX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (O28480_ARCFU | O28480)
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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  3qvx
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  O28480_ARCFU | O28480
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 Related Entries

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

UniProtKB/TrEMBL
        O28480_ARCFU | O28480: 1u1i 3qvs 3qvt 3qvw 3qw2

(-) Related Entries Specified in the PDB File

1rm0 L-MYO-INOSITOL 1-PHOSPHATE SYNTHASE FROM S.CEREVISIAE
1u1i L-MYO-INOSITOL 1-PHOSPHATE SYNTHASE FROM ARCHAEOGLOBUS FULGIDUS P1 FORM
3qvs L-MYO-INOSITOL 1-PHOSPHATE SYNTHASE FROM ARCHAEOGLOBUS FULGIDUS I222 FORM
3qvt MIPS FROM ARCHAEOGLOBUS FULGIDUS WILD-TYPE WITH THE INTERMEDIATE 5-KETO 1-PHOSPHO GLUCOSE
3qvw MIPS FROM ARCHAEOGLOBUS FULGIDUS MUTANT K278A
3qw2 MIPS FROM ARCHAEOGLOBUS FULGIDUS MUTANT N255A