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(-) Description

Title :  CRYSTAL STRUCTURE OF SHORT-CHAIN DEHYDROGENASE FROM PSEUDOMONAS SYRINGAE
 
Authors :  J. Osipiuk, X. Xu, H. Cui, B. Nocek, A. Savchenko, A. M. Edwards, A. Joach Midwest Center For Structural Genomics (Mcsg)
Date :  25 Feb 09  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Apc65077, Short-Chain Dehydrogenase, Oxidoreductase, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, X. Xu, H. Cui, B. Nocek, A. Savchenko, A. M. Edwards, A. Joachimiak
X-Ray Crystal Structure Of Short-Chain Dehydrogenase From Pseudomonas Syringae.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SHORT CHAIN DEHYDROGENASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B MODIFIED
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PSPPH_1072
    Organism Scientific: PSEUDOMONAS SYRINGAE PV. PHASEOLICOLA 1448A
    Organism Taxid: 264730
    Strain: 1448A / RACE 6

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric/Biological Unit (2, 16)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MSE15Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:12 , ALA B:13 , SER B:14 , SER B:35 , TYR B:36 , ARG B:37 , THR B:38 , HOH B:273 , HOH B:331 , HOH B:365BINDING SITE FOR RESIDUE ACT B 239

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:167 -Pro A:168
2Ala B:167 -Pro B:168
3Ala C:167 -Pro C:168
4Ala D:167 -Pro D:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GEM)

(-) 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:217
 aligned with Q48MN0_PSE14 | Q48MN0 from UniProtKB/TrEMBL  Length:236

    Alignment length:232
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234  
         Q48MN0_PSE14     5 SAPILITGASQRVGLHCALRLLEHGHRVIISYRTEHASVTELRQAGAVALYGDFSCETGIMAFIDLLKTQTSSLRAVVHNASEWLAETPGEEADNFTRMFSVHMLAPYLINLHCEPLLTASEVADIVHISDDVTRKGSSKHIAYCATKAGLESLTLSFAARFAPLVKVNGIAPALLMFQPKDDAAYRANALAKSALGIEPGAEVIYQSLRYLLDSTYVTGTTLTVNGGRHVK 236
               SCOP domains d3gema_ A: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains 3gemA00 A:5-236 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....hhhhhhhhhhhhhh...eeeee...hhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhh....eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....---------------........hhhhhhhhhhhhhh......eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gem A   5 SAPILITGASQRVGLHCALRLLEHGHRVIISYRTEHASVTELRQAGAVALYGDFSCETGImAFIDLLKTQTSSLRAVVHNASEWLAETPGEEADNFTRmFSVHmLAPYLINLHCEPLLTASEVADIVHISDDVTRKGSSKHIAYCATKAGLESLTLSFAARFAPLVKVNGIAPALLmF---------------SALGIEPGAEVIYQSLRYLLDSTYVTGTTLTVNGGRHVK 236
                                    14        24        34        44        54        64|       74        84        94       104   |   114       124       134       144       154       164       174      || -         -   |   204       214       224       234  
                                                                                       65-MSE                               103-MSE|                                                                      181-MSE          198                                      
                                                                                                                                 108-MSE                                                                   182                                                      


Chain B from PDB  Type:PROTEIN  Length:221
 aligned with Q48MN0_PSE14 | Q48MN0 from UniProtKB/TrEMBL  Length:236

    Alignment length:234
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    
         Q48MN0_PSE14     3 LSSAPILITGASQRVGLHCALRLLEHGHRVIISYRTEHASVTELRQAGAVALYGDFSCETGIMAFIDLLKTQTSSLRAVVHNASEWLAETPGEEADNFTRMFSVHMLAPYLINLHCEPLLTASEVADIVHISDDVTRKGSSKHIAYCATKAGLESLTLSFAARFAPLVKVNGIAPALLMFQPKDDAAYRANALAKSALGIEPGAEVIYQSLRYLLDSTYVTGTTLTVNGGRHVK 236
               SCOP domains d3gemb_ B: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 3gemB00 B:3-236 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee....hhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhh....eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....-------------...........hhhhhhhhhhhhhh......eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gem B   3 LSSAPILITGASQRVGLHCALRLLEHGHRVIISYRTEHASVTELRQAGAVALYGDFSCETGImAFIDLLKTQTSSLRAVVHNASEWLAETPGEEADNFTRmFSVHmLAPYLINLHCEPLLTASEVADIVHISDDVTRKGSSKHIAYCATKAGLESLTLSFAARFAPLVKVNGIAPALLm-------------LAKSALGIEPGAEVIYQSLRYLLDSTYVTGTTLTVNGGRHVK 236
                                    12        22        32        42        52        62  |     72        82        92       102|    | 112       122       132       142       152       162       172        |-         -  |    202       212       222       232    
                                                                                         65-MSE                               103-MSE|                                                                      181-MSE       195                                         
                                                                                                                                   108-MSE                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:224
 aligned with Q48MN0_PSE14 | Q48MN0 from UniProtKB/TrEMBL  Length:236

    Alignment length:232
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234  
         Q48MN0_PSE14     5 SAPILITGASQRVGLHCALRLLEHGHRVIISYRTEHASVTELRQAGAVALYGDFSCETGIMAFIDLLKTQTSSLRAVVHNASEWLAETPGEEADNFTRMFSVHMLAPYLINLHCEPLLTASEVADIVHISDDVTRKGSSKHIAYCATKAGLESLTLSFAARFAPLVKVNGIAPALLMFQPKDDAAYRANALAKSALGIEPGAEVIYQSLRYLLDSTYVTGTTLTVNGGRHVK 236
               SCOP domains d3gemc_ C: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains 3gemC00 C:5-236 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....hhhhhhhhhhhhhh...eeeee...hhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh....eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee..--------hhhhhhhhhhh.......hhhhhhhhhhhhhh......eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gem C   5 SAPILITGASQRVGLHCALRLLEHGHRVIISYRTEHASVTELRQAGAVALYGDFSCETGImAFIDLLKTQTSSLRAVVHNASEWLAETPGEEADNFTRmFSVHmLAPYLINLHCEPLLTASEVADIVHISDDVTRKGSSKHIAYCATKAGLESLTLSFAARFAPLVKVNGIAPAL--------AAYRANALAKSALGIEPGAEVIYQSLRYLLDSTYVTGTTLTVNGGRHVK 236
                                    14        24        34        44        54        64|       74        84        94       104   |   114       124       134       144       154       164       174    |    -   |   194       204       214       224       234  
                                                                                       65-MSE                               103-MSE|                                                                    179      188                                                
                                                                                                                                 108-MSE                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:214
 aligned with Q48MN0_PSE14 | Q48MN0 from UniProtKB/TrEMBL  Length:236

    Alignment length:232
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234  
         Q48MN0_PSE14     5 SAPILITGASQRVGLHCALRLLEHGHRVIISYRTEHASVTELRQAGAVALYGDFSCETGIMAFIDLLKTQTSSLRAVVHNASEWLAETPGEEADNFTRMFSVHMLAPYLINLHCEPLLTASEVADIVHISDDVTRKGSSKHIAYCATKAGLESLTLSFAARFAPLVKVNGIAPALLMFQPKDDAAYRANALAKSALGIEPGAEVIYQSLRYLLDSTYVTGTTLTVNGGRHVK 236
               SCOP domains d3gemd_ D: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains 3gemD00 D:5-236 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....hhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhh....eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhh.------------------hhhhhhhhhhhhhhhhh......eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gem D   5 SAPILITGASQRVGLHCALRLLEHGHRVIISYRTEHASVTELRQAGAVALYGDFSCETGImAFIDLLKTQTSSLRAVVHNASEWLAETPGEEADNFTRmFSVHmLAPYLINLHCEPLLTASEVADIVHISDDVTRKGSSKHIAYCATKAGLESLTLSFAARFAPLVKVNGIAPALLmFQP------------------EPGAEVIYQSLRYLLDSTYVTGTTLTVNGGRHVK 236
                                    14        24        34        44        54        64|       74        84        94       104   |   114       124       134       144       154       164       174      |184         -       204       214       224       234  
                                                                                       65-MSE                               103-MSE|                                                                      181-MSE               203                                 
                                                                                                                                 108-MSE                                                                     184
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q48MN0_PSE14 | Q48MN0)
molecular function
    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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    Ala D:167 - Pro D:168   [ RasMol ]  
 

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