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(-) Description

Title :  CRYSTAL STRUCTURE OF ALDOSE REDUCTASE A1-R COMPLEXED WITH NADP
 
Authors :  R. Takase, A. Ochiai, B. Mikami, W. Hashimoto, K. Murata
Date :  10 Mar 10  (Deposition) - 11 Aug 10  (Release) - 25 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Alpha/Beta/Alpha, Rossmann-Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Takase, A. Ochiai, B. Mikami, W. Hashimoto, K. Murata
Molecular Identification Of Unsaturated Uronate Reductase Prerequisite For Alginate Metabolism In Sphingomonas Sp. A1
Biochim. Biophys. Acta V. 1804 1925 2010
PubMed-ID: 20685299  |  Reference-DOI: 10.1016/J.BBAPAP.2010.05.010

(-) Compounds

Molecule 1 - CARBONYL REDUCTASE
    Chains: B, A, C, D
    EC Number: 1.1.1.126
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: A1-R
    Organism Scientific: SPHINGOMONAS SP.
    Organism Taxid: 90322
    Strain: A1
    Synonym: A1-R, 4-DEOXY-L-ERYTHRO-5-HEXOSEULOSE-URONIC ACID REDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1NAP4Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2TBU4Ligand/IonTERTIARY-BUTYL ALCOHOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:14 , SER B:16 , GLN B:17 , GLY B:18 , ILE B:19 , HIS B:37 , ARG B:39 , LYS B:40 , ALA B:64 , ASP B:65 , LEU B:66 , ASN B:92 , ALA B:93 , GLY B:94 , THR B:148 , GLY B:149 , SER B:150 , TYR B:164 , LYS B:168 , PRO B:194 , GLY B:195 , THR B:196 , VAL B:197 , THR B:199 , PHE B:201 , HIS B:202 , HOH B:2025 , HOH B:2041 , HOH B:2067 , HOH B:2073 , HOH B:2090 , HOH B:2116BINDING SITE FOR RESIDUE NAP B 3001
2AC2SOFTWAREASN B:177 , PHE B:181 , HIS B:182 , HOH B:2021 , PRO D:101 , LEU D:102 , GLY D:160BINDING SITE FOR RESIDUE TBU B 1001
3AC3SOFTWAREGLY A:14 , SER A:16 , GLN A:17 , GLY A:18 , ILE A:19 , HIS A:37 , ARG A:39 , LYS A:40 , ALA A:64 , ASP A:65 , LEU A:66 , ASN A:92 , ALA A:93 , GLY A:94 , THR A:148 , GLY A:149 , SER A:150 , TYR A:164 , LYS A:168 , PRO A:194 , GLY A:195 , THR A:196 , VAL A:197 , THR A:199 , PHE A:201 , HIS A:202 , HOH A:2036 , HOH A:2056 , HOH A:2061 , HOH A:2089 , HOH A:2095 , HOH A:2104BINDING SITE FOR RESIDUE NAP A 3001
4AC4SOFTWAREASN A:177 , PHE A:181 , HIS A:182 , HOH A:2024 , PRO C:101 , LEU C:102 , GLY C:160BINDING SITE FOR RESIDUE TBU A 1001
5AC5SOFTWAREGLY C:14 , SER C:16 , GLN C:17 , GLY C:18 , ILE C:19 , HIS C:37 , ARG C:39 , ALA C:64 , ASP C:65 , LEU C:66 , ASN C:92 , ALA C:93 , GLY C:94 , THR C:148 , GLY C:149 , SER C:150 , TYR C:164 , LYS C:168 , PRO C:194 , GLY C:195 , THR C:196 , VAL C:197 , THR C:199 , PHE C:201 , HIS C:202 , HOH C:2038 , HOH C:2053 , HOH C:2069 , HOH C:2082 , HOH C:2113 , HOH C:2171 , HOH C:2173 , HOH C:2207BINDING SITE FOR RESIDUE NAP C 3001
6AC6SOFTWAREPRO A:101 , LEU A:102 , GLY A:160 , ASN C:177 , PHE C:181 , HIS C:182 , HOH C:2013 , HOH C:2106BINDING SITE FOR RESIDUE TBU C 1001
7AC7SOFTWAREGLY D:14 , SER D:16 , GLN D:17 , GLY D:18 , ILE D:19 , HIS D:37 , ARG D:39 , ALA D:64 , ASP D:65 , LEU D:66 , ASN D:92 , ALA D:93 , GLY D:94 , THR D:148 , GLY D:149 , SER D:150 , TYR D:164 , LYS D:168 , PRO D:194 , GLY D:195 , THR D:196 , VAL D:197 , THR D:199 , PHE D:201 , HIS D:202 , HOH D:2026 , HOH D:2052 , HOH D:2059 , HOH D:2083 , HOH D:2090 , HOH D:2130 , HOH D:2153 , HOH D:2191BINDING SITE FOR RESIDUE NAP D 3001
8AC8SOFTWAREPRO B:101 , LEU B:102 , GLY B:160 , ASN D:177 , PHE D:181 , HIS D:182 , HOH D:2008 , HOH D:2097BINDING SITE FOR RESIDUE TBU D 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AFN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3AFN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AFN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AFN)

(-) Exons   (0, 0)

(no "Exon" information available for 3AFN)

(-) 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:257
 aligned with D6RU56_9SPHN | D6RU56 from UniProtKB/TrEMBL  Length:258

    Alignment length:257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
         D6RU56_9SPHN     2 FPDLKGKRVLITGSSQGIGLATARLFARAGAKVGLHGRKAPANIDETIASMRADGGDAAFFAADLATSEACQQLVDEFVAKFGGIDVLINNAGGLVGRKPLPEIDDTFYDAVMDANIRSVVMTTKFALPHLAAAAKASGQTSAVISTGSIAGHTGGGPGAGLYGAAKAFLHNVHKNWVDFHTKDGVRFNIVSPGTVDTAFHADKTQDVRDRISNGIPMGRFGTAEEMAPAFLFFASHLASGYITGQVLDINGGQYKH 258
               SCOP domains d3afna_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..eeee....hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhhh....eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3afn A   2 FPDLKGKRVLITGSSQGIGLATARLFARAGAKVGLHGRKAPANIDETIASMRADGGDAAFFAADLATSEACQQLVDEFVAKFGGIDVLINNAGGLVGRKPLPEIDDTFYDAVMDANIRSVVMTTKFALPHLAAAAKASGQTSAVISTGSIAGHTGGGPGAGLYGAAKAFLHNVHKNWVDFHTKDGVRFNIVSPGTVDTAFHADKTQDVRDRISNGIPMGRFGTAEEMAPAFLFFASHLASGYITGQVLDINGGQYKH 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       


Chain B from PDB  Type:PROTEIN  Length:257
 aligned with D6RU56_9SPHN | D6RU56 from UniProtKB/TrEMBL  Length:258

    Alignment length:257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
         D6RU56_9SPHN     2 FPDLKGKRVLITGSSQGIGLATARLFARAGAKVGLHGRKAPANIDETIASMRADGGDAAFFAADLATSEACQQLVDEFVAKFGGIDVLINNAGGLVGRKPLPEIDDTFYDAVMDANIRSVVMTTKFALPHLAAAAKASGQTSAVISTGSIAGHTGGGPGAGLYGAAKAFLHNVHKNWVDFHTKDGVRFNIVSPGTVDTAFHADKTQDVRDRISNGIPMGRFGTAEEMAPAFLFFASHLASGYITGQVLDINGGQYKH 258
               SCOP domains d3afnb_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..eeee....hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhhh....eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3afn B   2 FPDLKGKRVLITGSSQGIGLATARLFARAGAKVGLHGRKAPANIDETIASMRADGGDAAFFAADLATSEACQQLVDEFVAKFGGIDVLINNAGGLVGRKPLPEIDDTFYDAVMDANIRSVVMTTKFALPHLAAAAKASGQTSAVISTGSIAGHTGGGPGAGLYGAAKAFLHNVHKNWVDFHTKDGVRFNIVSPGTVDTAFHADKTQDVRDRISNGIPMGRFGTAEEMAPAFLFFASHLASGYITGQVLDINGGQYKH 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       


Chain C from PDB  Type:PROTEIN  Length:257
 aligned with D6RU56_9SPHN | D6RU56 from UniProtKB/TrEMBL  Length:258

    Alignment length:257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
         D6RU56_9SPHN     2 FPDLKGKRVLITGSSQGIGLATARLFARAGAKVGLHGRKAPANIDETIASMRADGGDAAFFAADLATSEACQQLVDEFVAKFGGIDVLINNAGGLVGRKPLPEIDDTFYDAVMDANIRSVVMTTKFALPHLAAAAKASGQTSAVISTGSIAGHTGGGPGAGLYGAAKAFLHNVHKNWVDFHTKDGVRFNIVSPGTVDTAFHADKTQDVRDRISNGIPMGRFGTAEEMAPAFLFFASHLASGYITGQVLDINGGQYKH 258
               SCOP domains d3afnc_ C: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..eeee....hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh..hhhhhhhhhh........hhhhhhhhhhhhhhhhhhh....eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3afn C   2 FPDLKGKRVLITGSSQGIGLATARLFARAGAKVGLHGRKAPANIDETIASMRADGGDAAFFAADLATSEACQQLVDEFVAKFGGIDVLINNAGGLVGRKPLPEIDDTFYDAVMDANIRSVVMTTKFALPHLAAAAKASGQTSAVISTGSIAGHTGGGPGAGLYGAAKAFLHNVHKNWVDFHTKDGVRFNIVSPGTVDTAFHADKTQDVRDRISNGIPMGRFGTAEEMAPAFLFFASHLASGYITGQVLDINGGQYKH 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       


Chain D from PDB  Type:PROTEIN  Length:257
 aligned with D6RU56_9SPHN | D6RU56 from UniProtKB/TrEMBL  Length:258

    Alignment length:257
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
         D6RU56_9SPHN     2 FPDLKGKRVLITGSSQGIGLATARLFARAGAKVGLHGRKAPANIDETIASMRADGGDAAFFAADLATSEACQQLVDEFVAKFGGIDVLINNAGGLVGRKPLPEIDDTFYDAVMDANIRSVVMTTKFALPHLAAAAKASGQTSAVISTGSIAGHTGGGPGAGLYGAAKAFLHNVHKNWVDFHTKDGVRFNIVSPGTVDTAFHADKTQDVRDRISNGIPMGRFGTAEEMAPAFLFFASHLASGYITGQVLDINGGQYKH 258
               SCOP domains d3afnd_ D: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..eeee....hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhh..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh....eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3afn D   2 FPDLKGKRVLITGSSQGIGLATARLFARAGAKVGLHGRKAPANIDETIASMRADGGDAAFFAADLATSEACQQLVDEFVAKFGGIDVLINNAGGLVGRKPLPEIDDTFYDAVMDANIRSVVMTTKFALPHLAAAAKASGQTSAVISTGSIAGHTGGGPGAGLYGAAKAFLHNVHKNWVDFHTKDGVRFNIVSPGTVDTAFHADKTQDVRDRISNGIPMGRFGTAEEMAPAFLFFASHLASGYITGQVLDINGGQYKH 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AFN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AFN)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (D6RU56_9SPHN | D6RU56)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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  3afn
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  1.1.1.126
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 Related Entries

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

UniProtKB/TrEMBL
        D6RU56_9SPHN | D6RU56: 3afm 4w7h

(-) Related Entries Specified in the PDB File

3afm APO-STRUCTURE OF THE SAME PROTEIN