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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE B
 
Authors :  S. Eswaramoorthy, S. Chamala, B. Evans, R. Foti, A. Gizzi, B. Hillerich J. Lafleur, R. Seidel, G. Villigas, W. Zencheck, S. C. Almo, S. Swamina York Structural Genomics Research Consortium (Nysgrc)
Date :  17 Nov 11  (Deposition) - 14 Dec 11  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nysgrc, Psi-Biology, Structural Genomics, New York Structural Genomics Research Consortium, Tim Barrel, Aldehyde Reductase, Xylose Reductase, Potassium Channel, Nadph-Dependent, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eswaramoorthy, S. C. Almo, S. Swaminathan
Crystal Structure Of A Putative 2, 5-Diketo-D-Gluconic Acid Reductase B
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE B
    Chains: A, B
    EC Number: 1.1.1.274
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DKGB, R00966, SMC00101
    Organism Common: ENSIFER MELILOTI
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 266834
    Strain: 1021

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:19 , TYR A:47 , HIS A:105 , TYR A:183 , HOH A:287 , TYR B:-4BINDING SITE FOR RESIDUE ACT A 276
2AC2SOFTWARETYR A:-4 , PHE B:19 , TYR B:47 , HIS B:105 , TYR B:183 , HOH B:285 , HOH B:305BINDING SITE FOR RESIDUE ACT B 276

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UP8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UP8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UP8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UP8)

(-) Exons   (0, 0)

(no "Exon" information available for 3UP8)

(-) 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:281
 aligned with Q92RC6_RHIME | Q92RC6 from UniProtKB/TrEMBL  Length:275

    Alignment length:281
                                  1                                                                                                                                                                                                                                                                                  
                                  |  4        14        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 
         Q92RC6_RHIME     - ------MHAVSSNGANIPALGFGTFRMSGAEVLRILPQALKLGFRHVDTAQIYGNEAEVGEAIQKSGIPRADVFLTTKVWVDNYRHDAFIASVDESLRKLRTDHVDLLLLHWPGSDVPMAERIGALNEVRNAGKVRHIGISNFNTTQMEEAARLSDAPIATNQVEYHPYLDQTKVLQTARRLGMSLTSYYAMANGKVPADPLLTEIGGRHGKTAAQVALRWLVQQQDVIVLSKTATEARLKENFAIFDFALTREEMAAVRELARPNGRIVNPQGLAPEWDA 275
               SCOP domains d3up8a_ A: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..ee......ee.eeee....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh..hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...eeeee...hhhhhhhhhh......hhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3up8 A  -5 LYFQSmmHAVSSNGANIPALGFGTFRmSGAEVLRILPQALKLGFRHVDTAQIYGNEAEVGEAIQKSGIPRADVFLTTKVWVDNYRHDAFIASVDESLRKLRTDHVDLLLLHWPGSDVPmAERIGALNEVRNAGKVRHIGISNFNTTQmEEAARLSDAPIATNQVEYHPYLDQTKVLQTARRLGmSLTSYYAmANGKVPADPLLTEIGGRHGKTAAQVALRWLVQQQDVIVLSKTATEARLKENFAIFDFALTREEmAAVRELARPNGRIVNPQGLAPEWDA 275
                                 ||  4        14      | 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 
                                 0-MSE               21-MSE                                                                                     113-MSE                      142-MSE                             178-MSE 186-MSE                                                         250-MSE                     
                                  1-MSE                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:281
 aligned with Q92RC6_RHIME | Q92RC6 from UniProtKB/TrEMBL  Length:275

    Alignment length:281
                                  1                                                                                                                                                                                                                                                                                  
                                  |  4        14        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 
         Q92RC6_RHIME     - ------MHAVSSNGANIPALGFGTFRMSGAEVLRILPQALKLGFRHVDTAQIYGNEAEVGEAIQKSGIPRADVFLTTKVWVDNYRHDAFIASVDESLRKLRTDHVDLLLLHWPGSDVPMAERIGALNEVRNAGKVRHIGISNFNTTQMEEAARLSDAPIATNQVEYHPYLDQTKVLQTARRLGMSLTSYYAMANGKVPADPLLTEIGGRHGKTAAQVALRWLVQQQDVIVLSKTATEARLKENFAIFDFALTREEMAAVRELARPNGRIVNPQGLAPEWDA 275
               SCOP domains d3up8b_ B: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eehhhhh.ee.eeee....hhhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhh.hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...eeeee...hhhhhhhhhh......hhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3up8 B  -5 LYFQSmmHAVSSNGANIPALGFGTFRmSGAEVLRILPQALKLGFRHVDTAQIYGNEAEVGEAIQKSGIPRADVFLTTKVWVDNYRHDAFIASVDESLRKLRTDHVDLLLLHWPGSDVPmAERIGALNEVRNAGKVRHIGISNFNTTQmEEAARLSDAPIATNQVEYHPYLDQTKVLQTARRLGmSLTSYYAmANGKVPADPLLTEIGGRHGKTAAQVALRWLVQQQDVIVLSKTATEARLKENFAIFDFALTREEmAAVRELARPNGRIVNPQGLAPEWDA 275
                                 ||  4        14      | 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 
                                 0-MSE               21-MSE                                                                                     113-MSE                      142-MSE                             178-MSE 186-MSE                                                         250-MSE                     
                                  1-MSE
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UP8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UP8)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q92RC6_RHIME | Q92RC6)
molecular function
    GO:0050580    2,5-didehydrogluconate reductase activity    Catalysis of the reaction: 2-dehydro-D-gluconate + NADP+ = 2,5-didehydro-D-gluconate + NADPH + H+.
    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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