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(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA THIC WITH BOUND IMIDAZOLE RIBONUCLEOTIDE, S-ADENOSYLHOMOCYSTEINE, FE4S4 CLUSTER AND ZN (TRIGONAL CRYSTAL FORM)
 
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 :  1.45
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
    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  (6, 7)

Asymmetric Unit (6, 7)
No.NameCountTypeFull Name
1BU12Ligand/Ion1,4-BUTANEDIOL
2CL1Ligand/IonCHLORIDE ION
3IRN1Ligand/Ion1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1H-IMIDAZOLE
4SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
5SF41Ligand/IonIRON/SULFUR CLUSTER
6ZN1Ligand/IonZINC ION
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1BU14Ligand/Ion1,4-BUTANEDIOL
2CL-1Ligand/IonCHLORIDE ION
3IRN2Ligand/Ion1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1H-IMIDAZOLE
4SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
5SF42Ligand/IonIRON/SULFUR CLUSTER
6ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:570 , MET A:572 , CYS A:573 , CYS A:578 , SER A:579 , SAH A:703 , CL A:705BINDING SITE FOR RESIDUE SF4 A 701
2AC2SOFTWAREASN A:228 , MET A:257 , LEU A:259 , TYR A:286 , THR A:320 , 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 , LEU A:451 , SAH A:703 , HOH A:879BINDING SITE FOR RESIDUE IRN A 702
3AC3SOFTWAREASN A:228 , ILE A:229 , GLY A:230 , ASN A:231 , LEU A:259 , VAL A:341 , ARG A:343 , ARG A:386 , HIS A:426 , GLU A:489 , HIS A:490 , LEU A:493 , PRO A:494 , MET A:572 , CYS A:573 , SF4 A:701 , IRN A:702 , ZN A:704 , HOH A:862 , HOH A:863 , HOH A:870 , HOH A:875 , HOH A:922 , HOH A:1148BINDING SITE FOR RESIDUE SAH A 703
4AC4SOFTWAREHIS A:426 , HIS A:490 , SAH A:703 , HOH A:1148 , HOH A:1149BINDING SITE FOR RESIDUE ZN A 704
5AC5SOFTWAREHIS A:490 , SF4 A:701 , HOH A:1312BINDING SITE FOR RESIDUE CL A 705
6AC6SOFTWAREARG A:305 , ILE A:309 , GLN A:374 , HOH A:866BINDING SITE FOR RESIDUE BU1 A 706
7AC7SOFTWAREVAL A:113 , PRO A:114 , PHE A:115 , THR A:183 , HOH A:825BINDING SITE FOR RESIDUE BU1 A 707

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S25)

(-) 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 4S25)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S25)

(-) Exons   (0, 0)

(no "Exon" information available for 4S25)

(-) 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:513
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               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.......hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh....eeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.eeee.......hhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh....eeee..........hhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhh...hhhhhhh..........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s25 A  79 SPDFQPIPSFEECFPKSTKEHKEVVHEESGHVLKVPFRRVHLSGGEPAFDNYDTSGPQNVNAHIGLAKLRKEWIDRREKLGTPRYTQMYYAKQGIITEEMLYCATREKLDPEFVRSEVARGRAIIPSNKKHLELEPMIVGRKFLVKVNANIGNSAVASSIEEEVYKVQWATMWGADTIMDLSTGRHIHETREWILRNSAVPVGTVPIYQALEKVDGIAENLNWEVFRETLIEQAEQGVDYFTIHAGVLLRYIPLTAKRLTGIVSRGGSIHAKWCLAYHKENFAYEHWDDILDICNQYDVALSIGDGLRPGSIYDANDTAQFAELLTQGELTRRAWEKDVQVMNEGPGHVPMHKIPENMQKQLEWCNEAPFYTLGPLTTDIAPGYDHITSAIGAANIGALGTALLCYVTPKEHLGLPNRDDVKAGVIAYKIAAHAADLAKQHPHAQAWDDALSKARFEFRWMDQFALSLDPMTAMSFHDETLPADGAKVAHFCSMCGPKFCSMKITEDIRKYAE 591
                                    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       538       548       558       568       578       588
   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 4S25)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S25)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S25)

(-) Gene Ontology  (11, 11)

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    Gly A:452 - Pro A:453   [ RasMol ]  
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  4s25
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  4.1.99.17
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 Related Entries

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

UniProtKB/Swiss-Prot
        THIC_ARATH | O82392: 4n7q 4s26 4s27 4s28 4s29

(-) Related Entries Specified in the PDB File

3epm 3epn 3epo 4n7q 4s26 4s27 4s28 4s29 4s2a