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(-) Description

Title :  THE CRYSTAL STRUCTURE OF L-SORBOSE REDUCTASE FROM GLUCONOBACTER FRATEURII COMPLEXED WITH NADPH AND L-SORBOSE
 
Authors :  K. Kubota, K. Nagata, M. Okai, K. Miyazono, M. Tanokura
Date :  07 May 10  (Deposition) - 09 Feb 11  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,C,E,G
Keywords :  Rossmann-Fold, Nadph-Dependent Reductase, Short Chain Dehydrogenase/Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kubota, K. Nagata, M. Okai, K. Miyazono, W. Soemphol, J. Ohtsuka, A. Yamamura, N. Saichana, H. Toyama, K. Matsushita, M. Tanokura
The Crystal Structure Of L-Sorbose Reductase From Gluconobacter Frateurii Complexed With Nadph And L-Sorbose
J. Mol. Biol. V. 407 543 2011
PubMed-ID: 21277857  |  Reference-DOI: 10.1016/J.JMB.2011.01.008

(-) Compounds

Molecule 1 - NADPH-SORBOSE REDUCTASE
    Chains: A, C, E, G
    EC Number: 1.1.1.289
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SBOA
    Mutation: YES
    Organism Scientific: GLUCONOBACTER FRATEURII
    Organism Taxid: 38308
    Synonym: L-SORBOSE REDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ACEG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2SOE4Ligand/IonALPHA-L-SORBOPYRANOSE
3SOL5Ligand/IonL-SORBOSE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESOL A:0 , GLY A:14 , SER A:16 , SER A:17 , GLY A:18 , ILE A:19 , ALA A:38 , ARG A:39 , GLN A:40 , ARG A:43 , VAL A:64 , ASP A:65 , VAL A:66 , ASN A:92 , GLY A:94 , LEU A:115 , ASN A:142 , ALA A:143 , SER A:144 , TYR A:157 , LYS A:161 , PRO A:187 , GLY A:188 , ILE A:190 , THR A:192 , TRP A:195 , HOH A:276 , HOH A:310 , HOH A:315BINDING SITE FOR RESIDUE NDP A 270
02AC2SOFTWAREGLY A:96 , SER A:144 , ILE A:145 , LEU A:151 , TYR A:153 , GLU A:154 , TYR A:157 , GLY A:188 , TRP A:195 , NDP A:270BINDING SITE FOR RESIDUE SOL A 0
03AC3SOFTWARESOL C:0 , GLY C:14 , SER C:16 , SER C:17 , GLY C:18 , ILE C:19 , ALA C:38 , ARG C:39 , GLN C:40 , ARG C:43 , VAL C:64 , ASP C:65 , VAL C:66 , ASN C:92 , GLY C:94 , LEU C:115 , ASN C:142 , ALA C:143 , TYR C:157 , LYS C:161 , PRO C:187 , GLY C:188 , ILE C:190 , THR C:192 , PRO C:193 , TRP C:195 , HOH C:285 , HOH C:298 , HOH C:431 , HOH C:453 , HOH C:489BINDING SITE FOR RESIDUE NDP C 270
04AC4SOFTWAREGLY C:96 , SER C:144 , ILE C:145 , TYR C:153 , GLU C:154 , TYR C:157 , TRP C:195 , NDP C:270 , HOH C:589BINDING SITE FOR RESIDUE SOL C 0
05AC5SOFTWARESOL E:0 , GLY E:14 , SER E:16 , SER E:17 , GLY E:18 , ILE E:19 , ALA E:38 , ARG E:39 , GLN E:40 , ARG E:43 , VAL E:64 , ASP E:65 , VAL E:66 , ASN E:92 , ALA E:93 , GLY E:94 , LEU E:115 , ASN E:142 , ALA E:143 , SER E:144 , TYR E:157 , LYS E:161 , PRO E:187 , GLY E:188 , ILE E:190 , THR E:192 , TRP E:195 , HOH E:291 , HOH E:296 , HOH E:301 , HOH E:321 , HOH E:353BINDING SITE FOR RESIDUE NDP E 270
06AC6SOFTWAREGLY E:96 , SER E:144 , ILE E:145 , GLU E:154 , TYR E:157 , NDP E:270 , HOH E:590BINDING SITE FOR RESIDUE SOL E 0
07AC7SOFTWAREGLY E:4 , ILE E:5 , LYS E:8 , ILE E:88 , GLY E:137 , ASN E:179 , ARG E:181 , CYS E:241 , GLU E:243 , HOH E:320BINDING SITE FOR RESIDUE SOE E 264
08AC8SOFTWAREVAL A:148 , ALA A:252 , PHE A:254 , LEU A:263 , ALA E:252 , LEU E:263 , HOH E:327BINDING SITE FOR RESIDUE SOL E 265
09AC9SOFTWARESOL G:0 , GLY G:14 , SER G:16 , SER G:17 , GLY G:18 , ILE G:19 , ALA G:38 , ARG G:39 , GLN G:40 , ARG G:43 , VAL G:64 , ASP G:65 , VAL G:66 , ASN G:92 , GLY G:94 , LEU G:115 , ASN G:142 , ALA G:143 , TYR G:157 , LYS G:161 , PRO G:187 , GLY G:188 , ILE G:190 , THR G:192 , TRP G:195 , HOH G:294 , HOH G:452 , HOH G:470 , HOH G:521BINDING SITE FOR RESIDUE NDP G 270
10BC1SOFTWAREGLY G:96 , SER G:144 , ILE G:145 , CYS G:146 , TYR G:153 , GLU G:154 , TYR G:157 , GLY G:188 , TRP G:195 , NDP G:270BINDING SITE FOR RESIDUE SOL G 0
11BC2SOFTWAREVAL C:41 , HIS C:45 , HIS G:45 , ALA G:48 , ARG G:49 , LYS G:52 , VAL G:59 , GLU G:61 , HOH G:281 , HOH G:414BINDING SITE FOR RESIDUE SOE G 264
12BC3SOFTWAREGLY G:4 , ILE G:5 , LYS G:8 , ILE G:88 , GLY G:137 , ASN G:179 , ARG G:181 , CYS G:241 , GLU G:243 , HOH G:488BINDING SITE FOR RESIDUE SOE G 265
13BC4SOFTWAREALA C:252 , PHE C:254 , LEU C:263 , ALA G:252 , PHE G:254 , LEU G:260 , LEU G:263 , HOH G:272 , HOH G:416BINDING SITE FOR RESIDUE SOE G 266

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AI3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3AI3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AI3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AI3)

(-) Exons   (0, 0)

(no "Exon" information available for 3AI3)

(-) 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:263
 aligned with A4PB64_9PROT | A4PB64 from UniProtKB/TrEMBL  Length:263

    Alignment length:263
                                    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   
         A4PB64_9PROT     1 MDMGISGKVAVITGSSSGIGLAIAEGFAKEGAHIVLVARQVDRLHEAARSLKEKFGVRVLEVAVDVATPEGVDAVVESVRSSFGGADILVNNAGTGSNETIMEAADEKWQFYWELHVMAAVRLARGLVPGMRARGGGAIIHNASICAVQPLWYEPIYNVTKAALMMFSKTLATEVIKDNIRVNCINPGLILTPDWIKTAKELTKDNGGDWKGYLQSVADEHAPIKRFASPEELANFFVFLCSERATYSVGSAYFVDGGMLKTL 263
               SCOP domains d3ai3a_ A: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhh..........eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ai3 A   1 MDMGISGKVAVITGSSSGIGLAIAEGFAKEGAHIVLVARQVDRLHEAARSLKEKFGVRVLEVAVDVATPEGVDAVVESVRSSFGGADILVNNAGTGSNETIMEAADEKWQFYWELLVMAAVRLARGLVPGMRARGGGAIIHNASICAVQPLWYEPIYNVTKAALMMFSKTLATEVIKDNIRVNCINPGLILTPDWIKTAKELTKDNGGDWKGYLQSVADEHAPIKRFASPEELANFFVFLCSERATYSVGSAYFVDGGMLKTL 263
                                    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   


Chain C from PDB  Type:PROTEIN  Length:263
 aligned with A4PB64_9PROT | A4PB64 from UniProtKB/TrEMBL  Length:263

    Alignment length:263
                                    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   
         A4PB64_9PROT     1 MDMGISGKVAVITGSSSGIGLAIAEGFAKEGAHIVLVARQVDRLHEAARSLKEKFGVRVLEVAVDVATPEGVDAVVESVRSSFGGADILVNNAGTGSNETIMEAADEKWQFYWELHVMAAVRLARGLVPGMRARGGGAIIHNASICAVQPLWYEPIYNVTKAALMMFSKTLATEVIKDNIRVNCINPGLILTPDWIKTAKELTKDNGGDWKGYLQSVADEHAPIKRFASPEELANFFVFLCSERATYSVGSAYFVDGGMLKTL 263
               SCOP domains d3ai3c_ C: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhhhhhhhhh..........eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ai3 C   1 MDMGISGKVAVITGSSSGIGLAIAEGFAKEGAHIVLVARQVDRLHEAARSLKEKFGVRVLEVAVDVATPEGVDAVVESVRSSFGGADILVNNAGTGSNETIMEAADEKWQFYWELLVMAAVRLARGLVPGMRARGGGAIIHNASICAVQPLWYEPIYNVTKAALMMFSKTLATEVIKDNIRVNCINPGLILTPDWIKTAKELTKDNGGDWKGYLQSVADEHAPIKRFASPEELANFFVFLCSERATYSVGSAYFVDGGMLKTL 263
                                    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   


Chain E from PDB  Type:PROTEIN  Length:263
 aligned with A4PB64_9PROT | A4PB64 from UniProtKB/TrEMBL  Length:263

    Alignment length:263
                                    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   
         A4PB64_9PROT     1 MDMGISGKVAVITGSSSGIGLAIAEGFAKEGAHIVLVARQVDRLHEAARSLKEKFGVRVLEVAVDVATPEGVDAVVESVRSSFGGADILVNNAGTGSNETIMEAADEKWQFYWELHVMAAVRLARGLVPGMRARGGGAIIHNASICAVQPLWYEPIYNVTKAALMMFSKTLATEVIKDNIRVNCINPGLILTPDWIKTAKELTKDNGGDWKGYLQSVADEHAPIKRFASPEELANFFVFLCSERATYSVGSAYFVDGGMLKTL 263
               SCOP domains d3ai3e_ E: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhh..........eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ai3 E   1 MDMGISGKVAVITGSSSGIGLAIAEGFAKEGAHIVLVARQVDRLHEAARSLKEKFGVRVLEVAVDVATPEGVDAVVESVRSSFGGADILVNNAGTGSNETIMEAADEKWQFYWELLVMAAVRLARGLVPGMRARGGGAIIHNASICAVQPLWYEPIYNVTKAALMMFSKTLATEVIKDNIRVNCINPGLILTPDWIKTAKELTKDNGGDWKGYLQSVADEHAPIKRFASPEELANFFVFLCSERATYSVGSAYFVDGGMLKTL 263
                                    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   


Chain G from PDB  Type:PROTEIN  Length:263
 aligned with A4PB64_9PROT | A4PB64 from UniProtKB/TrEMBL  Length:263

    Alignment length:263
                                    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   
         A4PB64_9PROT     1 MDMGISGKVAVITGSSSGIGLAIAEGFAKEGAHIVLVARQVDRLHEAARSLKEKFGVRVLEVAVDVATPEGVDAVVESVRSSFGGADILVNNAGTGSNETIMEAADEKWQFYWELHVMAAVRLARGLVPGMRARGGGAIIHNASICAVQPLWYEPIYNVTKAALMMFSKTLATEVIKDNIRVNCINPGLILTPDWIKTAKELTKDNGGDWKGYLQSVADEHAPIKRFASPEELANFFVFLCSERATYSVGSAYFVDGGMLKTL 263
               SCOP domains d3ai3g_ G: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhhhhhhhhhh..........eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ai3 G   1 MDMGISGKVAVITGSSSGIGLAIAEGFAKEGAHIVLVARQVDRLHEAARSLKEKFGVRVLEVAVDVATPEGVDAVVESVRSSFGGADILVNNAGTGSNETIMEAADEKWQFYWELLVMAAVRLARGLVPGMRARGGGAIIHNASICAVQPLWYEPIYNVTKAALMMFSKTLATEVIKDNIRVNCINPGLILTPDWIKTAKELTKDNGGDWKGYLQSVADEHAPIKRFASPEELANFFVFLCSERATYSVGSAYFVDGGMLKTL 263
                                    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
   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 3AI3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AI3)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C,E,G   (A4PB64_9PROT | A4PB64)
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.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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        A4PB64_9PROT | A4PB64: 3ai1 3ai2

(-) Related Entries Specified in the PDB File

3ai1 3ai2