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(-) Description

Title :  CRYSTAL STRUCTURE OF DAAO(Y228L/R283G) VARIANT (R-2-PHENYLPYRROLIDINE BINDING FORM)
 
Authors :  S. Nakano, K. Yasukawa, N. Kawahara, E. Ishitsubo, H. Tokiwa, Y. Asano
Date :  03 Mar 15  (Deposition) - 06 Apr 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Amine Oxidase, Variant Of D-Amino Acid Oxidase, R-2-Phenylpyrrolidine Binding Form, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Nakano, K. Yasukawa, N. Kawahara, E. Ishitsubo, H. Tokiwa, Y. Asano
Crystal Structure Of Daao Variant
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - D-AMINO-ACID OXIDASE
    Chains: A
    EC Number: 1.4.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-340
    Gene: DAO
    Mutation: YES
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: DAO
 
Molecule 2 - D-AMINO-ACID OXIDASE
    Chains: B
    EC Number: 1.4.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-340
    Gene: DAO
    Mutation: YES
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: DAO

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
196B2Ligand/Ion(2R)-2-PHENYLPYRROLIDINE
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:224 , ILE A:230 , PHE A:242 , GLY A:313 , FAD A:402binding site for residue 96B A 401
2AC2SOFTWAREGLY A:7 , ALA A:8 , GLY A:9 , VAL A:10 , ILE A:11 , ALA A:36 , ASP A:37 , ARG A:38 , THR A:43 , THR A:44 , THR A:45 , ALA A:48 , ALA A:49 , GLY A:50 , LEU A:51 , ARG A:162 , LYS A:163 , VAL A:164 , CYS A:181 , THR A:182 , GLY A:183 , ILE A:202 , GLY A:281 , HIS A:311 , GLY A:312 , GLY A:313 , TYR A:314 , GLY A:315 , LEU A:316 , THR A:317 , 96B A:401 , HOH A:501 , HOH A:502 , HOH A:504binding site for residue FAD A 402
3AC3SOFTWAREARG A:286 , GLN A:288 , VAL A:289 , GLU A:292 , ARG B:22 , LYS B:328binding site for residue SO4 A 403
4AC4SOFTWARELEU B:51 , TYR B:224 , ILE B:230 , GLY B:313 , FAD B:402binding site for residue 96B B 401
5AC5SOFTWAREGLY B:7 , ALA B:8 , GLY B:9 , VAL B:10 , ILE B:11 , ALA B:36 , ASP B:37 , ARG B:38 , THR B:43 , THR B:44 , THR B:45 , ALA B:48 , ALA B:49 , GLY B:50 , LEU B:51 , ARG B:162 , LYS B:163 , VAL B:164 , CYS B:181 , THR B:182 , GLY B:183 , TRP B:185 , ILE B:202 , GLY B:281 , HIS B:311 , GLY B:312 , GLY B:313 , TYR B:314 , GLY B:315 , LEU B:316 , THR B:317 , 96B B:401 , HOH B:503 , HOH B:504 , HOH B:506binding site for residue FAD B 402
6AC6SOFTWAREHIS B:24 , ARG B:155binding site for residue SO4 B 403
7AC7SOFTWAREASP A:37 , ARG A:38 , ARG B:142 , GLN B:146binding site for residue SO4 B 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gln A:28 -Pro A:29
2Thr A:40 -Pro A:41
3Gln B:28 -Pro B:29
4Thr B:40 -Pro B:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YJH)

(-) Sequences/Alignments

Asymmetric/Biological 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:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh......eeeeee......hhhhhh.............hhhhhhhhhhhhhhhh......hhhh.eeeeeeeeee.............eeeee.hhhhhh......eeeeeeeeeehhhhhhhhhhhhhhhh..eeee....hhhhhhhh...eeee.hhhhhhhh......eeeeeeeeeee......eeee...........eeee....eeee...ee.......hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee.......eeeeee..eeeeeee......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yjh A   1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDVKVYADRFTPFTTTDVAAGLWQPYTSEPSNPQEANWNQQTFNYLLSHIGSPNAANMGLTPVSGYNLFREAVPDPYWKDMVLGFRKLTPRELDMFPDYRYGWFNTSLILEGRKYLQWLTERLTERGVKFFLRKVESFEEVARGGADVIINCTGVWAGVLQPDPLLQPGRGQIIKVDAPWLKNFIITHDLERGIYNSPLIIPGLQAVTLGGTFQVGNWNEINNIQDHNTIWEGCCRLEPTLKDAKIVGEYTGFGPVRPQVRLEREQLRFGSSNTEVIHNYGHGGYGLTIHWGCALEVAKLFGKVLEERNLLAA 342
                                    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       260       270       280       290       300       310       320       330       340  


Chain B from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh......eeeeee......hhhhhh............hhhhhhhhhhhhhhhhhhh....hhhh.eeeeeeeeee.............eeeee.hhhhhh......eeeeeeeeeehhhhhhhhhhhhhhhh..eeee....hhhhhhhh...eeee.hhhhhhhh......eeeeeeeeeee......eeee...........eeee....eeee...ee.......hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee.......eeeee....eeeeee......hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yjh B   1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDVKVYADRFTPFTTTDVAAGLWQPYTSEPSNPQEANWNQQTFNYLLSHIGSPNAANMGLTPVSGYNLFREAVPDPYWKDMVLGFRKLTPRELDMFPDYRYGWFNTSLILEGRKYLQWLTERLTERGVKFFLRKVESFEEVARGGADVIINCTGVWAGVLQPDPLLQPGRGQIIKVDAPWLKNFIITHDLERGIYNSPLIIPGLQAVTLGGTFQVGNWNEINNIQDHNTIWEGCCRLEPTLKDAKIVGEYTGFGPVRPQVRLEREQLRFGSSNTEVIHNYGHGGYGLTIHWGCALEVAKLFGKVLEERNLL 340
                                    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       260       270       280       290       300       310       320       330       340
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 4YJH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln A:28 - Pro A:29   [ RasMol ]  
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    Thr B:40 - Pro B:41   [ RasMol ]  
 

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  1.4.3.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        OXDA_PIG | P00371: 1an9 1dao 1ddo 1evi 1kif 1ve9 3wgt 4yjd 4yjf 4yjg

(-) Related Entries Specified in the PDB File

4yjd 4yjf 4yjg