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(-) Description

Title :  CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PDX1-I320 COMPLEX FROM MULTIPLE CRYSTALS
 
Authors :  M. J. Rodrigues, V. Windeisen, Y. Zhang, G. Guedez, S. Weber, M. Strohme J. W. Hanes, A. Royant, G. Evans, I. Sinning, S. E. Ealick, T. P. Begley,
Date :  06 Aug 16  (Deposition) - 18 Jan 17  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (3x)
Keywords :  Beta/Alpha Barrel, Pyridoxal Phosphate Synthase, Glutamine Amidotransferase, Vitamin B6 Biosythesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Rodrigues, V. Windeisen, Y. Zhang, G. Guedez, S. Weber, M. Strohmeier, J. W. Hanes, A. Royant, G. Evans, I. Sinning, S. E. Ealick, T. P. Begley, I. Tews
Lysine Relay Mechanism Coordinates Intermediate Transfer In Vitamin B6 Biosynthesis.
Nat. Chem. Biol. V. 13 290 2017
PubMed-ID: 28092359  |  Reference-DOI: 10.1038/NCHEMBIO.2273

(-) Compounds

Molecule 1 - PYRIDOXAL 5'-PHOSPHATE SYNTHASE SUBUNIT PDX1.3
    Chains: A, B, C, D
    EC Number: 4.3.3.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A-D(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PLP SYNTHASE SUBUNIT PDX1.3
    Gene: PDX13, GIP2, PDX1L3, RSR4, AT5G01410, T10O8.120
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PLP SYNTHASE SUBUNIT PDX1.3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1KIK4Ligand/Ion(4~{S})-4-AZANYL-5-OXIDANYL-PENT-1-EN-3-ONE
2PO44Ligand/IonPHOSPHATE ION
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 36)
No.NameCountTypeFull Name
1KIK12Ligand/Ion(4~{S})-4-AZANYL-5-OXIDANYL-PENT-1-EN-3-ONE
2PO412Ligand/IonPHOSPHATE ION
3SO412Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:66 , LYS A:166 , GLU A:168 , GLY A:170 , GLY A:231 , GLY A:252 , SER A:253 , KIK A:403 , HOH A:502 , HOH A:505 , HOH A:563binding site for residue PO4 A 401
02AC2SOFTWAREHIS A:132 , GLU A:151 , ARG A:154 , ARG A:155 , HOH A:538 , HOH A:573 , LYS D:204 , HOH D:569binding site for residue SO4 A 402
03AC3SOFTWAREASP A:41 , LYS A:98 , SER A:121 , VAL A:123 , ARG A:164 , LYS A:166 , PHE A:250 , PO4 A:401binding site for residue KIK A 403
04AC4SOFTWAREPRO B:66 , LYS B:166 , GLU B:168 , GLY B:170 , GLY B:231 , GLY B:252 , SER B:253 , KIK B:403 , HOH B:546binding site for residue PO4 B 401
05AC5SOFTWAREHIS B:132 , GLU B:151 , ARG B:154 , ARG B:155 , HOH B:596 , LYS C:204 , HOH C:544binding site for residue SO4 B 402
06AC6SOFTWAREPRO C:66 , LYS C:166 , GLU C:168 , GLY C:170 , GLY C:230 , GLY C:231 , GLY C:252 , SER C:253 , KIK C:403 , HOH C:523 , HOH C:546binding site for residue PO4 C 401
07AC7SOFTWARELYS B:204 , HOH B:539 , HIS C:132 , GLU C:151 , ARG C:154 , ARG C:155 , HOH C:507 , HOH C:566 , HOH C:569binding site for residue SO4 C 402
08AC8SOFTWAREPRO D:66 , LYS D:166 , GLU D:168 , ALA D:169 , GLY D:170 , GLY D:230 , GLY D:231 , GLY D:252 , SER D:253 , KIK D:403 , HOH D:529binding site for residue PO4 D 401
09AC9SOFTWARELYS A:204 , HOH A:559 , HIS D:132 , GLU D:151 , ARG D:154 , ARG D:155 , HOH D:506 , HOH D:566 , HOH D:595binding site for residue SO4 D 402
10AD1SOFTWAREASP B:41 , MET B:60 , ALA B:61 , ALA B:97 , ALA B:99 , LEU B:110 , ASP B:119 , SER B:121 , VAL B:123 , ARG B:164 , LYS B:166 , PO4 B:401 , HOH B:511binding site for Di-peptide KIK B 403 and LYS B 98
11AD2SOFTWAREASP B:41 , LYS B:98 , SER B:121 , GLU B:122 , VAL B:123 , CYS B:146 , ARG B:164 , THR B:165 , GLY B:167 , ALA B:169 , HIS B:180 , ALA B:229 , PO4 B:401binding site for Di-peptide KIK B 403 and LYS B 166
12AD3SOFTWAREASP C:41 , LYS C:98 , SER C:121 , GLU C:122 , VAL C:123 , CYS C:146 , ARG C:164 , THR C:165 , GLY C:167 , HIS C:180 , ALA C:229 , PO4 C:401binding site for Di-peptide KIK C 403 and LYS C 166
13AD4SOFTWAREASP C:41 , MET C:60 , ALA C:61 , MET C:78 , ALA C:97 , ALA C:99 , LEU C:110 , ASP C:119 , SER C:121 , VAL C:123 , LEU C:124 , ARG C:164 , LYS C:166 , PO4 C:401 , HOH C:510binding site for Di-peptide KIK C 403 and LYS C 98
14AD5SOFTWAREASP D:41 , LYS D:98 , SER D:121 , GLU D:122 , VAL D:123 , CYS D:146 , ARG D:164 , THR D:165 , GLY D:167 , ALA D:169 , HIS D:180 , ALA D:229 , GLY D:230 , PO4 D:401binding site for Di-peptide KIK D 403 and LYS D 166
15AD6SOFTWAREASP D:41 , MET D:60 , ALA D:61 , ALA D:97 , ALA D:99 , ASP D:119 , SER D:121 , VAL D:123 , LEU D:124 , ARG D:164 , LYS D:166 , PO4 D:401 , HOH D:573binding site for Di-peptide KIK D 403 and LYS D 98

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LNV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LNV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LNV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LNV)

(-) Exons   (0, 0)

(no "Exon" information available for 5LNV)

(-) 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:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh..eeee...hhhhhhhhh......hhhhhhhhhhhh...eeeee...hhhhhhhhhhhh..eeee.............hhhhh...eeeee.hhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhh....eeeee....hhhhhhhhhhh....eee........hhhhhhhhhhhhhhh..hhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lnv A  22 SPFSVKVGLAQMLRGGVIMDVVNAEQARIAEEAGACAVMALERVPADIRAQGGVARMSDPQMIKEIKQAVTIPVMAKARIGHFVEAQILEAIGIDYIDESEVLTLADEDHHINKHNFRIPFVCGCRNLGEALRRIREGAAMIRTKGEAGTGNIIEAVRHVRSVNGDIRVLRNMDDDEVFTFAKKLAAPYDLVMQTKQLGRLPVVQFAAGGVATPADAALMMQLGCDGVFVGSGIFKSGDPARRARAIVQAVTHYSDPEMLVEVSCGLGEAMVGINLN 298
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....eeeee.hhhhhhhhhhh...eeee...hhhhhhhhh......hhhhhhhhhhh....eeeee...hhhhhhhhhhhh..eeee.............hhhhh...eeeee.hhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhh....eeeee....hhhhhhhhhhh....eeehhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lnv B  21 KSPFSVKVGLAQMLRGGVIMDVVNAEQARIAEEAGACAVMALERVPADIRAQGGVARMSDPQMIKEIKQAVTIPVMAKARIGHFVEAQILEAIGIDYIDESEVLTLADEDHHINKHNFRIPFVCGCRNLGEALRRIREGAAMIRTKGEAGTGNIIEAVRHVRSVNGDIRVLRNMDDDEVFTFAKKLAAPYDLVMQTKQLGRLPVVQFAAGGVATPADAALMMQLGCDGVFVGSGIFKSGDPARRARAIVQAVTHYSDPEMLVEVSCGLGEAMVGINLN 298
                                    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        


Chain C from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eeeeee.hhhhhhhhhhhh..eeee...hhhhhhhhh......hhhhhhhhhhh....eeeeee..hhhhhhhhhhhh..eeeee............hhhhh...eeeee.hhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhh..hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lnv C  22 SPFSVKVGLAQMLRGGVIMDVVNAEQARIAEEAGACAVMALERVPADIRAQGGVARMSDPQMIKEIKQAVTIPVMAKARIGHFVEAQILEAIGIDYIDESEVLTLADEDHHINKHNFRIPFVCGCRNLGEALRRIREGAAMIRTKGEAGTGNIIEAVRHVRSVNGDIRVLRNMDDDEVFTFAKKLAAPYDLVMQTKQLGRLPVVQFAAGGVATPADAALMMQLGCDGVFVGSGIFKSGDPARRARAIVQAVTHYSDPEMLVEVSCGLGEAMVGINL 297
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      


Chain D from PDB  Type:PROTEIN  Length:275
                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....eeeee.hhhhhhhhhhhh..eeee...hhhhhhhhh......hhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh..eeeee............hhhhh...eeeee.hhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeeehhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lnv D  23 PFSVKVGLAQMLRGGVIMDVVNAEQARIAEEAGACAVMALERVPADIRAQGGVARMSDPQMIKEIKQAVTIPVMAKARIGHFVEAQILEAIGIDYIDESEVLTLADEDHHINKHNFRIPFVCGCRNLGEALRRIREGAAMIRTKGEAGTGNIIEAVRHVRSVNGDIRVLRNMDDDEVFTFAKKLAAPYDLVMQTKQLGRLPVVQFAAGGVATPADAALMMQLGCDGVFVGSGIFKSGDPARRARAIVQAVTHYSDPEMLVEVSCGLGEAMVGINL 297
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292
   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 5LNV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LNV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LNV)

(-) Gene Ontology  (22, 22)

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  4.3.3.6
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        PDX13_ARATH | Q8L940: 5k2z 5k3v 5lnr 5lns 5lnu 5lnw

(-) Related Entries Specified in the PDB File

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