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(-) Description

Title :  CRYSTAL STRUCTURE OF A MYO-INOSITOL-1-PHOSPHATE SYNTHASE-RELATED PROTEIN (TM_1419) FROM THERMOTOGA MARITIMA MSB8 AT 1.70 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  11 Mar 08  (Deposition) - 25 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Myo-Inositol-1-Phosphate Synthase-Related Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Myo-Inositol-1-Phosphate Synthase-Related Protein (Tm1419) From Thermotoga Maritima At 1. 70 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MYO-INOSITOL-1-PHOSPHATE SYNTHASE-RELATED PROTEIN
    Atcc: 43589
    Chains: A
    EC Number: 5.5.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MH1
    Expression System Strain: DL41
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1419, TM_1419
    Organism Scientific: THERMOTOGA MARITIMA MSB8
    Organism Taxid: 243274
    Strain: MSB8 / DSM 3109 / JCM 10099

 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, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MG1Ligand/IonMAGNESIUM ION
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:212 , ARG A:229 , HOH A:506BINDING SITE FOR RESIDUE CL A 383
2AC2SOFTWAREALA A:218 , ASP A:219 , SER A:222 , PRO A:363 , ARG A:364BINDING SITE FOR RESIDUE CL A 384
3AC3SOFTWAREALA A:213 , ASN A:238 , LYS A:290 , HOH A:433BINDING SITE FOR RESIDUE CL A 385
4AC4SOFTWAREASN A:189 , PRO A:354 , PRO A:356 , GLU A:359 , HOH A:401 , HOH A:402BINDING SITE FOR RESIDUE MG A 386
5AC5SOFTWAREGLY A:8 , GLN A:9 , GLY A:10 , TYR A:11 , ASP A:53 , LYS A:58 , SER A:91 , THR A:130 , CYS A:131 , THR A:132 , THR A:133 , ALA A:159 , TYR A:163 , ILE A:183 , ASP A:208 , THR A:211 , MET A:243 , ASP A:244 , ASP A:316 , LEU A:320 , HOH A:411 , HOH A:416 , HOH A:421 , HOH A:426 , HOH A:474 , HOH A:563BINDING SITE FOR RESIDUE NAD A 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:206 -Asp A:207
2Gly A:355 -Pro A:356

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CIN)

(-) 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:382
 aligned with Q9X1D6_THEMA | Q9X1D6 from UniProtKB/TrEMBL  Length:382

    Alignment length:382
                             1                                                                                                                                                                                                                                                                                                                                                                                            
                             |       9        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  
         Q9X1D6_THEMA     - -MVKVLILGQGYVASTFVAGLEKLRKGEIEPYGVPLARELPIGFEDIKIVGSYDVDRAKIGKKLSEVVKQYWNDVDSLTSDPEIRKGVHLGSVRNLPIEAEGLEDSMTLKEAVDTLVKEWTELDPDVIVNTCTTEAFVPFGNKEDLLKAIENNDKERLTATQVYAYAAALYANKRGGAAFVNVIPTFIANDPAFVELAKENNLVVFGDDGATGATPFTADVLSHLAQRNRYVKDVAQFNIGGNMDFLALTDDGKNKSKEFTKSSIVKDILGYDAPHYIKPTGYLEPLGDKKFIAIHIEYVSFNGATDELMINGRINDSPALGGLLVDLVRLGKIALDRKEFGTVYPVNAFYMKNPGPAEEKNIPRIIAYEKMRIWAGLKPKW 381
               SCOP domains d3cina1 A:0-209,A:317-381 Hypothetical protein TM1419                                                                                                                                                             d3cina2 A:210-316 Hypothetical protein TM1419                                                              d3cina1 A:0-209,A:317-381 Hypothetical protein TM1419             SCOP domains
               CATH domains 3cinA01 A:0-211,A:316-381 NAD(P)-binding Rossmann-like Domain                                                                                                                                                       3cinA02 A:212-315 Dihydrodipicolinate Reductase; domain 2                                               3cinA01 A:0-211,A:316-381 NAD(P)-binding Rossmann-like Domain      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhh................hhh.eeeeeeee........hhhhhhhhhh............ee...............hhhhh.hhhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhhh.eeee......hhhhhhhhhhhhhhhh..eeeeeeeeeee.hhhhhh.hhhhhhhhhhhhh.hhhhhhhh....ee....ee.hhhh.eeeeeeeeeee.hhh.eeeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhh...........hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cin A   0 HMVKVLILGQGYVASTFVAGLEKLRKGEIEPYGVPLARELPIGFEDIKIVGSYDVDRAKIGKKLSEVVKQYWNDVDSLTSDPEIRKGVHLGSVRNLPIEAEGLEDSMTLKEAVDTLVKEWTELDPDVIVNTCTTEAFVPFGNKEDLLKAIENNDKERLTATQVYAYAAALYANKRGGAAFVNVIPTFIANDPAFVELAKENNLVVFGDDGATGATPFTADVLSHLAQRNRYVKDVAQFNIGGNMDFLALTDDGKNKSKEFTKSSIVKDILGYDAPHYIKPTGYLEPLGDKKFIAIHIEYVSFNGATDELMINGRINDSPALGGLLVDLVRLGKIALDRKEFGTVYPVNAFYMKNPGPAEEKNIPRIIAYEKMRIWAGLKPKW 381
                                     9        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
   Legend:   → Mismatch (orange background)
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  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 3CIN)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9X1D6_THEMA | Q9X1D6)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.

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