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(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA THIC WITH BOUND AMINOIMIDAZOLE RIBONUCLEOTIDE, 5'-DEOXYADENOSINE, L-METHIONINE, FE4S4 CLUSTER AND FE
 
Authors :  M. K. Fenwick, A. P. Mehta, Y. Zhang, S. Abdelwahed, T. P. Begley, S. E. Ea
Date :  19 Jan 15  (Deposition) - 08 Apr 15  (Release) - 08 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.27
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alpha-Beta Barrel, Radical Sam Superfamily, Iron-Sulfur Cluster, Thiamin, Vitamin B1, Vitamin B12, Domain Swapping, Adomet And Glutamate Mutase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Fenwick, A. P. Mehta, Y. Zhang, S. H. Abdelwahed, T. P. Begley, S. E. Ealick
Non-Canonical Active Site Architecture Of The Radical Sam Thiamin Pyrimidine Synthase.
Nat Commun V. 6 6480
PubMed-ID: 25813242  |  Reference-DOI: 10.1038/NCOMMS7480

(-) Compounds

Molecule 1 - PHOSPHOMETHYLPYRIMIDINE SYNTHASE, CHLOROPLASTIC
    Chains: A
    EC Number: 4.1.99.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 72-644
    Gene: THIC, PY, AT2G29630, T27A16.27
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: HYDROXYMETHYLPYRIMIDINE PHOSPHATE SYNTHASE, HMP-P SYNTHASE, HMP-PHOSPHATE SYNTHASE, HMPP SYNTHASE, PROTEIN PYRIMIDINE REQUIRING, THIAMINE BIOSYNTHESIS PROTEIN THIC, PROTEIN THIAMINE C

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 8)

Asymmetric Unit (7, 8)
No.NameCountTypeFull Name
15AD1Ligand/Ion5'-DEOXYADENOSINE
2AIR1Ligand/Ion5-AMINOIMIDAZOLE RIBONUCLEOTIDE
3BU12Ligand/Ion1,4-BUTANEDIOL
4CL1Ligand/IonCHLORIDE ION
5FE21Ligand/IonFE (II) ION
6MET1Mod. Amino AcidMETHIONINE
7SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (6, 14)
No.NameCountTypeFull Name
15AD2Ligand/Ion5'-DEOXYADENOSINE
2AIR2Ligand/Ion5-AMINOIMIDAZOLE RIBONUCLEOTIDE
3BU14Ligand/Ion1,4-BUTANEDIOL
4CL-1Ligand/IonCHLORIDE ION
5FE22Ligand/IonFE (II) ION
6MET2Mod. Amino AcidMETHIONINE
7SF42Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:570 , MET A:572 , CYS A:573 , CYS A:578 , SER A:579 , MET A:704 , CL A:706BINDING SITE FOR RESIDUE SF4 A 701
2AC2SOFTWAREASN A:228 , MET A:257 , LEU A:259 , TYR A:286 , HIS A:322 , SER A:342 , ARG A:343 , GLY A:344 , ASP A:383 , ARG A:386 , GLU A:422 , GLY A:423 , TYR A:449 , CYS A:483 , 5AD A:703 , HOH A:878BINDING SITE FOR RESIDUE AIR A 702
3AC3SOFTWAREASN A:228 , ILE A:229 , GLY A:230 , ASN A:231 , LEU A:259 , ARG A:343 , ARG A:386 , LEU A:451 , GLU A:489 , LEU A:493 , MET A:572 , AIR A:702 , HOH A:861 , HOH A:862 , HOH A:874 , HOH A:920BINDING SITE FOR RESIDUE 5AD A 703
4AC4SOFTWAREVAL A:341 , ARG A:386 , HIS A:426 , LEU A:451 , GLU A:489 , HIS A:490 , CYS A:573 , SF4 A:701 , FE2 A:705 , HOH A:869 , HOH A:1181BINDING SITE FOR RESIDUE MET A 704
5AC5SOFTWAREHIS A:426 , HIS A:490 , MET A:704 , HOH A:1181 , HOH A:1182BINDING SITE FOR RESIDUE FE2 A 705
6AC6SOFTWAREHIS A:490 , SF4 A:701 , HOH A:1301BINDING SITE FOR RESIDUE CL A 706
7AC7SOFTWAREARG A:305 , HOH A:865BINDING SITE FOR RESIDUE BU1 A 707
8AC8SOFTWAREVAL A:113 , PRO A:114 , PHE A:115 , THR A:183 , ARG A:184 , HOH A:824BINDING SITE FOR RESIDUE BU1 A 708

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S27)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:424 -Gly A:425
2Gly A:452 -Pro A:453

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S27)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S27)

(-) Exons   (0, 0)

(no "Exon" information available for 4S27)

(-) 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:515
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh..eeeeeeeeee....eeeeeeeeee........eee..................hhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhh..ee..............ee.....eeeeee.......hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh....eeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.eeee.......hhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhh...hhhhhhh..........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s27 A  78 SSPDFQPIPSFEECFPKSTKEHKEVVHEESGHVLKVPFRRVHLSGGEPAFDNYDTSGPQNVNAHIGLAKLRKEWIDRREKLGTPRYTQMYYAKQGIITEEMLYCATREKLDPEFVRSEVARGRAIIPSNKKHLELEPMIVGRKFLVKVNANIGNSAVASSIEEEVYKVQWATMWGADTIMDLSTGRHIHETREWILRNSAVPVGTVPIYQALEKVDGIAENLNWEVFRETLIEQAEQGVDYFTIHAGVLLRYIPLTAKRLTGIVSRGGSIHAKWCLAYHKENFAYEHWDDILDICNQYDVALSIGDGLRPGSIYDANDTAQFAELLTQGELTRRAWEKDVQVMNEGPGHVPMHKIPENMQKQLEWCNEAPFYTLGPLTTDIAPGYDHITSAIGAANIGALGTALLCYVTPKEHLGLPNRDDVKAGVIAYKIAAHAADLAKQHPHAQAWDDALSKARFEFRWMDQFALSLDPMTAMSFHDETLPADGAKVAHFCSMCGPKFCSMKITEDIRKYAEM 704
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587   ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           591|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            704
   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  (0, 0)

(no "SCOP Domain" information available for 4S27)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S27)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S27)

(-) Gene Ontology  (11, 11)

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  4s27
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 Related Entries

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UniProtKB/Swiss-Prot
        THIC_ARATH | O82392: 4n7q 4s25 4s26 4s28 4s29

(-) Related Entries Specified in the PDB File

3epm 3epn 3epo 4n7q 4s25 4s26 4s28 4s29 4s2a