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(-) Description

Title :  CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE ARABINOSE DEHYDROGENASE ARA1 COMPLEXED WITH NADPH
 
Authors :  X. Q. Hu, P. C. Guo, W. F. Li, C. Z. Zhou
Date :  23 Dec 12  (Deposition) - 27 Nov 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Tim Barrel, Dehydrogenase, Nadph Binding, Cytosol, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Q. Hu, P. C. Guo, J. D. Ma, W. F. Li
Structures Of Saccharomyces Cerevisiaed-Arabinose Dehydrogenase Ara1 And Its Complex With Nadph: Implications For Cofactor-Assisted Substrate Recognition
Acta Crystallogr. , Sect. F V. 69 1190 2013
PubMed-ID: 24192347  |  Reference-DOI: 10.1107/S1744309113026857

(-) Compounds

Molecule 1 - D-ARABINOSE DEHYDROGENASE [NAD(P)+] HEAVY CHAIN
    Chains: A, C
    EC Number: 1.1.1.117
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ARA1, YBR1127, YBR149W
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: S288C
    Synonym: AKR3C, NADP+ DEPENDENT ARABINOSE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:39 , THR A:40 , ALA A:41 , ASP A:66 , TYR A:71 , HIS A:131 , SER A:192 , ASN A:193 , GLN A:214 , TYR A:240 , SER A:241 , PRO A:242 , LEU A:243 , GLY A:244 , SER A:245 , ALA A:248 , LEU A:251 , ASN A:268 , ILE A:283 , PRO A:284 , ARG A:285 , SER A:286 , LEU A:287 , ARG A:291 , HOH A:586 , HOH A:594BINDING SITE FOR RESIDUE NDP A 401
2AC2SOFTWAREGLY C:39 , THR C:40 , ALA C:41 , ASP C:66 , TYR C:71 , HIS C:131 , TRP C:132 , SER C:192 , ASN C:193 , GLN C:214 , TYR C:240 , SER C:241 , PRO C:242 , LEU C:243 , GLY C:244 , SER C:245 , ALA C:248 , LEU C:251 , ASN C:268 , ILE C:283 , PRO C:284 , ARG C:285 , SER C:286 , LEU C:287 , ARG C:291 , HOH C:617BINDING SITE FOR RESIDUE NDP C 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:17 -Pro A:18
2His C:17 -Pro C:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IJR)

(-) 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:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4ijra_ A: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eee.....eee...ee...hhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhh...hhhhheeeeeehhhhh.hhhhhhhhhhhhhh.....eeee.............hhhhh.................hhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..ee.....hhhhhhhh......hhhhhhhhhhhhhhh......hhhhh..........hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ijr A  15 MLHPKTTEIYFSLNNGVRIPALGLGTANPHEKLAETKQAVKAAIKAGYRHIDTAWAYETEPFVGEAIKELLEDGSIKREDLFITTKVWPVLWDEVDRSLNESLKALGLEYVDLLLQHWPLCFEKIKDPKGISGLVKTPVDDSGKTMYAADGDYLETYKQLEKIYLDPNDHRVRAIGVSNFSIEYLERLIKECRVKPTVNQVETHPHLPQMELRKFCFMHDILLTAYSPLGSHGAPNLKIPLVKKLAEKYNVTGNDLLISYHIRQGTIVIPRSLNPVRISSSIEFASLTKDELQELNDFGEKYPVRFIDEPFAAILPEFTGNGPNLDNL 342
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334        


Chain C from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4ijrc_ C: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eee.....eee...ee...hhhhhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh...hhhhheeeeeehhhhh.hhhhhhhhhhhhhh.....eeee.............hhhhh..................hhhhhhhhhhhhhh........eeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..ee.....hhhhhhhh......hhhhhhhhhhhhhhh......hhhhh..........hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ijr C  15 MLHPKTTEIYFSLNNGVRIPALGLGTANPHEKLAETKQAVKAAIKAGYRHIDTAWAYETEPFVGEAIKELLEDGSIKREDLFITTKVWPVLWDEVDRSLNESLKALGLEYVDLLLQHWPLCFEKIKDPKGISGLVKTPVDDSGKTMYAADGDYLETYKQLEKIYLDPNDHRVRAIGVSNFSIEYLERLIKECRVKPTVNQVETHPHLPQMELRKFCFMHDILLTAYSPLGSHGAPNLKIPLVKKLAEKYNVTGNDLLISYHIRQGTIVIPRSLNPVRISSSIEFASLTKDELQELNDFGEKYPVRFIDEPFAAILPEFTGNGPNLDNL 342
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        ARA1_YEAST | P38115: 4ijc

(-) Related Entries Specified in the PDB File

4ijc