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(-) Description

Title :  HUMAN SEPIAPTERIN REDUCTASE IN COMPLEX WITH THE COFACTOR NADP+ AND THE TRYPTHOPHAN METABOLITE XANTHURENIC ACID
 
Authors :  K. Johnsson
Date :  31 Mar 15  (Deposition) - 18 Nov 15  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Sepiapterin-Reductase, Xanthurenic Acid, Inhibitor, Tryptophan- Metabolite, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Haruki, R. Hovius, M. G. Pedersen, K. Johnsson
Tetrahydrobiopterin Biosynthesis As A Potential Target Of The Kynurenine Pathway Metabolite Xanthurenic Acid.
J. Biol. Chem. V. 291 652 2016
PubMed-ID: 26565027  |  Reference-DOI: 10.1074/JBC.C115.680488

(-) Compounds

Molecule 1 - SEPIAPTERIN REDUCTASE
    Chains: A, B, C, D
    EC Number: 1.1.1.153
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET9A
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SPR
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THE N-TERMINAL MHHHHHHENLYFQGMEG IS NOT RESOLVED IN THE STRUCTURE & IS COMPOSED OF A HIS_6 TAG;
TEV CLEAVAGE SITE;
MEG ARE THE 1ST 3 RESIDUES OF THE WT PROTEIN. THE C-TERMINAL K IS NOT VISIBLE IN THE STRUCTURE.
    Synonym: SPR

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
14KL4Ligand/IonXANTHURIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4SO46Ligand/IonSULFATE ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
14KL2Ligand/IonXANTHURIC ACID
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4SO43Ligand/IonSULFATE ION
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
14KL2Ligand/IonXANTHURIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
3NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
4SO43Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:11 , SER A:13 , ARG A:14 , GLY A:15 , PHE A:16 , ALA A:38 , ARG A:39 , ASN A:40 , ALA A:65 , ASP A:66 , LEU A:67 , ASN A:97 , ALA A:98 , GLY A:99 , LEU A:123 , ILE A:152 , SER A:153 , TYR A:167 , LYS A:171 , PRO A:195 , GLY A:196 , PRO A:197 , LEU A:198 , THR A:200 , ASP A:201 , MET A:202 , GLN A:203 , 4KL A:802 , HOH A:907 , HOH A:910 , HOH A:917 , HOH A:930binding site for residue NAP A 801
02AC2SOFTWARESER A:154 , LEU A:155 , TRP A:164 , TYR A:167 , GLN A:203 , LEU A:219 , NAP A:801 , HOH A:901 , HOH A:908 , HOH A:915binding site for residue 4KL A 802
03AC3SOFTWAREARG A:39binding site for residue SO4 A 803
04AC4SOFTWAREGLY B:11 , SER B:13 , ARG B:14 , GLY B:15 , PHE B:16 , ALA B:38 , ARG B:39 , ASN B:40 , ALA B:65 , ASP B:66 , LEU B:67 , ASN B:97 , ALA B:98 , GLY B:99 , LEU B:123 , ILE B:152 , SER B:153 , TYR B:167 , LYS B:171 , PRO B:195 , GLY B:196 , PRO B:197 , LEU B:198 , THR B:200 , MET B:202 , GLN B:203 , 4KL B:302 , HOH B:406 , HOH B:410binding site for residue NAP B 301
05AC5SOFTWARESER B:154 , LEU B:155 , TRP B:164 , TYR B:167 , PRO B:197 , GLN B:203 , NAP B:301 , HOH B:401 , HOH B:402 , HOH B:403 , HOH B:418binding site for residue 4KL B 302
06AC6SOFTWARELYS C:87 , GLY C:88binding site for residue SO4 B 303
07AC7SOFTWAREARG B:39 , HOH B:413 , HOH B:427binding site for residue SO4 B 304
08AC8SOFTWARELYS B:217 , GLN B:220binding site for residue EDO B 305
09AC9SOFTWAREGLY C:11 , SER C:13 , ARG C:14 , GLY C:15 , PHE C:16 , ALA C:38 , ARG C:39 , ASN C:40 , ALA C:65 , ASP C:66 , LEU C:67 , ASN C:97 , ILE C:152 , SER C:153 , TYR C:167 , LYS C:171 , PRO C:195 , GLY C:196 , PRO C:197 , LEU C:198 , THR C:200 , ASP C:201 , MET C:202 , GLN C:203 , 4KL C:302 , HOH C:409 , HOH C:413 , HOH C:415 , HOH C:431binding site for residue NAP C 301
10AD1SOFTWARESER C:154 , LEU C:155 , TRP C:164 , TYR C:167 , PRO C:197 , GLN C:203 , LEU C:219 , NAP C:301 , SO4 C:304 , HOH C:401 , HOH C:405 , HOH C:410binding site for residue 4KL C 302
11AD2SOFTWAREARG C:39binding site for residue SO4 C 303
12AD3SOFTWARECYS C:156 , PHE C:161 , TRP C:164 , MET C:215 , 4KL C:302 , HOH C:401binding site for residue SO4 C 304
13AD4SOFTWAREGLY D:11 , SER D:13 , ARG D:14 , GLY D:15 , PHE D:16 , ALA D:38 , ARG D:39 , ASN D:40 , ALA D:65 , ASP D:66 , LEU D:67 , ASN D:97 , ALA D:98 , GLY D:99 , LEU D:123 , ILE D:152 , SER D:153 , TYR D:167 , LYS D:171 , PRO D:195 , GLY D:196 , PRO D:197 , LEU D:198 , THR D:200 , MET D:202 , GLN D:203 , 4KL D:302 , HOH D:410 , HOH D:427 , HOH D:429binding site for residue NAP D 301
14AD5SOFTWARESER D:154 , LEU D:155 , TRP D:164 , TYR D:167 , PRO D:197 , GLN D:203 , NAP D:301 , SO4 D:303 , HOH D:401 , HOH D:403 , HOH D:408 , HOH D:422binding site for residue 4KL D 302
15AD6SOFTWARECYS D:156 , PHE D:161 , TRP D:164 , MET D:215 , 4KL D:302binding site for residue SO4 D 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z3K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Z3K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z3K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z3K)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z3K)

(-) 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:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh........eeeeee..........hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z3k A   1 GLGRAVCLLTGASRGFGRTLAPLLASLLSPGSVLVLSARNDEALRQLEAELGAERSGLRVVRVPADLGAEAGLQQLLGALRELPRPKGLQRLLLINNAGSLGDVSKGFVDLSDSTQVNNYWALNLTSMLCLTSSVLKAFPDSPGLNRTVVNISSLCALQPFKGWALYCAGKAARDMLFQVLALEEPNVRVLNYAPGPLDTDMQQLARETSVDPDMRKGLQELKAKGKLVDCKVSAQKLLSLLEKDEFKSGAHVDFYD 257
                                    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       


Chain B from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhhhhheeeeeee....hhhhhhhhhhhhhh........eeeeee..........hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z3k B   1 GLGRAVCLLTGASRGFGRTLAPLLASLLSPGSVLVLSARNDEALRQLEAELGAERSGLRVVRVPADLGAEAGLQQLLGALRELPRPKGLQRLLLINNAGSLGDVSKGFVDLSDSTQVNNYWALNLTSMLCLTSSVLKAFPDSPGLNRTVVNISSLCALQPFKGWALYCAGKAARDMLFQVLALEEPNVRVLNYAPGPLDTDMQQLARETSVDPDMRKGLQELKAKGKLVDCKVSAQKLLSLLEKDEFKSGAHVDFYD 257
                                    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       


Chain C from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhh.......eeeeee..........hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh......eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z3k C   1 GLGRAVCLLTGASRGFGRTLAPLLASLLSPGSVLVLSARNDEALRQLEAELGAERSGLRVVRVPADLGAEAGLQQLLGALRELPRPKGLQRLLLINNAGSLGDVSKGFVDLSDSTQVNNYWALNLTSMLCLTSSVLKAFPDSPGLNRTVVNISSLCALQPFKGWALYCAGKAARDMLFQVLALEEPNVRVLNYAPGPLDTDMQQLARETSVDPDMRKGLQELKAKGKLVDCKVSAQKLLSLLEKDEFKSGAHVDFYD 257
                                    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       


Chain D from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....hhhhhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhh........eeeeee..........hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z3k D   1 GLGRAVCLLTGASRGFGRTLAPLLASLLSPGSVLVLSARNDEALRQLEAELGAERSGLRVVRVPADLGAEAGLQQLLGALRELPRPKGLQRLLLINNAGSLGDVSKGFVDLSDSTQVNNYWALNLTSMLCLTSSVLKAFPDSPGLNRTVVNISSLCALQPFKGWALYCAGKAARDMLFQVLALEEPNVRVLNYAPGPLDTDMQQLARETSVDPDMRKGLQELKAKGKLVDCKVSAQKLLSLLEKDEFKSGAHVDFYD 257
                                    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
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

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(no "SCOP Domain" information available for 4Z3K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z3K)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (12, 12)

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        SPRE_HUMAN | P35270: 1z6z 4hwk 4j7u 4j7x 4xwy

(-) Related Entries Specified in the PDB File

4xwy 4XWY CONTAINS THE SAME PROTEIN, BUT COMPLEXED WITH ANOTHER LIGAND