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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SHORT CHAIN DEHYDROGENASE FROM SHIGELLA FLEXNERI
 
Authors :  Y. Kim, X. Xu, H. Cui, A. Savchenko, A. Edwards, A. Joachimiak, Midwest For Structural Genomics (Mcsg)
Date :  23 Aug 08  (Deposition) - 23 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta-Alpha Sandwich, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, X. Xu, H. Cui, A. Savchenko, A. Edwards, A. Joachimiak
Crystal Structure Of The Short Chain Dehydrogenase From Shigella Flexneri
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SHORT-CHAIN DEHYDROGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21DE3
    Expression System Vector Type: PLASMID
    Gene: YCIK, S1358, SF1273
    Organism Scientific: SHIGELLA FLEXNERI 2A
    Organism Taxid: 198214
    Strain: 301

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 30)

Asymmetric/Biological Unit (5, 30)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3MSE22Mod. Amino AcidSELENOMETHIONINE
4SO44Ligand/IonSULFATE ION
5ZN1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:19 , ALA B:20 , SER B:21 , GLY B:43 , ARG B:44 , ASN B:45 , HOH B:364 , HOH B:472 , HOH B:500BINDING SITE FOR RESIDUE SO4 B 253
2AC2SOFTWAREGLY A:19 , ALA A:20 , SER A:21 , ASP A:22 , GLY A:43 , ARG A:44 , ASN A:45 , HOH A:336 , HOH A:372BINDING SITE FOR RESIDUE SO4 A 253
3AC3SOFTWARESER B:153 , GLY B:195 , GLY B:196 , ARG B:202 , ARG B:246 , PRO B:248 , GLY B:249 , HOH B:355 , HOH B:405 , HOH B:449 , HOH B:477BINDING SITE FOR RESIDUE SO4 B 254
4AC4SOFTWARESER A:153 , GLY A:195 , GLY A:196 , ARG A:202 , ARG A:246 , PRO A:248 , GLY A:249 , HOH A:294 , HOH A:347 , HOH A:427 , HOH A:428BINDING SITE FOR RESIDUE SO4 A 254
5AC5SOFTWAREASP A:22 , GLY A:23 , ARG A:26 , ALA A:200 , HOH A:303 , HOH A:328BINDING SITE FOR RESIDUE EDO A 255
6AC6SOFTWAREGLN A:118 , THR B:75 , SER B:76 , ARG B:234BINDING SITE FOR RESIDUE EDO A 256
7AC7SOFTWARETYR B:3 , TYR B:35 , LEU B:225 , HOH B:324 , HOH B:344 , HOH B:487BINDING SITE FOR RESIDUE GOL B 255
8AC8SOFTWAREARG B:34 , GLU B:59BINDING SITE FOR RESIDUE ZN B 256

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E9Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3E9Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E9Q)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.YCIK_ECOLI152-180
 		  2A:152-180
B:152-180

(-) Exons   (0, 0)

(no "Exon" information available for 3E9Q)

(-) 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:255
 aligned with Q83RM3_SHIFL | Q83RM3 from UniProtKB/TrEMBL  Length:252

    Alignment length:255
                               1                                                                                                                                                                                                                                                           
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247     
         Q83RM3_SHIFL     - ---MHYQPKQDLLNDRIILVTGASDGIGREAAMTYARYGATVILLGRNEEKLRQVASHINEETGRQPQWFILDLLTCTSENCQQLAQRIVVNYPRLDGVLHNAGLLGDVCPMSEQNPQVWQDVMQINVNATFMLTQALLPLLLKSDAGSLVFTSSSVGRQGRANWGAYAASKFATEGMMQVLADEYQQRLRVNCINPGGTRTAMRASAFPTEDPQKLKTPADIMPLYLWLMGDDSRRKTGMTFDAQPGRKPGISQ 252
               SCOP domains d3e9qa_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3e9qA00 A:-2-252 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhh......eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhh.....eee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e9q A  -2 FQGmHYQPKQDLLNDRIILVTGASDGIGREAAmTYARYGATVILLGRNEEKLRQVASHINEETGRQPQWFILDLLTCTSENCQQLAQRIVVNYPRLDGVLHNAGLLGDVCPmSEQNPQVWQDVmQINVNATFmLTQALLPLLLKSDAGSLVFTSSSVGRQGRANWGAYAASKFATEGmmQVLADEYQQRLRVNCINPGGTRTAmRASAFPTEDPQKLKTPADImPLYLWLmGDDSRRKTGmTFDAQPGRKPGISQ 252
                               |     7        17        27  |     37        47        57        67        77        87        97       107 |     117   |   127  |    137       147       157       167       177       187       197   |   207       217   |   227|      237|      247     
                               |                           30-MSE                                                                        109-MSE     121-MSE  130-MSE                                      175-MSE                   201-MSE             221-MSE  |       238-MSE          
                               1-MSE                                                                                                                                                                        176-MSE                                             228-MSE                    


Chain A from PDB  Type:PROTEIN  Length:255
 aligned with YCIK_ECOLI | P31808 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:255
                               1                                                                                                                                                                                                                                                           
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247     
           YCIK_ECOLI     - ---MHYQPKQDLLNDRIILVTGASDGIGREAAMTYARYGATVILLGRNEEKLRQVASHINEETGRQPQWFILDLLTCTSENCQQLAQRIAVNYPRLDGVLHNAGLLGDVCPMSEQNPQVWQDVMQVNVNATFMLTQALLPLLLKSDAGSLVFTSSSVGRQGRANWGAYAASKFATEGMMQVLADEYQQRLRVNCINPGGTRTAMRASAFPTEDPQKLKTPADIMPLYLWLMGDDSRRKTGMTFDAQPGRKPGISQ 252
               SCOP domains d3e9qa_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3e9qA00 A:-2-252 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhh......eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhh.....eee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:152-180    ------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e9q A  -2 FQGmHYQPKQDLLNDRIILVTGASDGIGREAAmTYARYGATVILLGRNEEKLRQVASHINEETGRQPQWFILDLLTCTSENCQQLAQRIVVNYPRLDGVLHNAGLLGDVCPmSEQNPQVWQDVmQINVNATFmLTQALLPLLLKSDAGSLVFTSSSVGRQGRANWGAYAASKFATEGmmQVLADEYQQRLRVNCINPGGTRTAmRASAFPTEDPQKLKTPADImPLYLWLmGDDSRRKTGmTFDAQPGRKPGISQ 252
                               |     7        17        27  |     37        47        57        67        77        87        97       107 |     117   |   127  |    137       147       157       167       177       187       197   |   207       217   |   227|      237|      247     
                               1-MSE                       30-MSE                                                                        109-MSE     121-MSE  130-MSE                                      175-MSE                   201-MSE             221-MSE  |       238-MSE          
                                                                                                                                                                                                            176-MSE                                             228-MSE                    


Chain B from PDB  Type:PROTEIN  Length:256
 aligned with Q83RM3_SHIFL | Q83RM3 from UniProtKB/TrEMBL  Length:252

    Alignment length:256
                                  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      
         Q83RM3_SHIFL     - ------MHYQPKQDLLNDRIILVTGASDGIGREAAMTYARYGATVILLGRNEEKLRQVASHINEETGRQPQWFILDLLTCTSENCQQLAQRIVVNYPRLDGVLHNAGLLGDVCPMSEQNPQVWQDVMQINVNATFMLTQALLPLLLKSDAGSLVFTSSSVGRQGRANWGAYAASKFATEGMMQVLADEYQQRLRVNCINPGGTRTAMRASAFPTEDPQKLKTPADIMPLYLWLMGDDSRRKTGMTFDAQPGRKPGI 250
               SCOP domains d3e9qb_ B: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3e9qB00 B:-5-250 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhh....eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhh.....eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e9q B  -5 NLYFQGmHYQPKQDLLNDRIILVTGASDGIGREAAmTYARYGATVILLGRNEEKLRQVASHINEETGRQPQWFILDLLTCTSENCQQLAQRIVVNYPRLDGVLHNAGLLGDVCPmSEQNPQVWQDVmQINVNATFmLTQALLPLLLKSDAGSLVFTSSSVGRQGRANWGAYAASKFATEGmmQVLADEYQQRLRVNCINPGGTRTAmRASAFPTEDPQKLKTPADImPLYLWLmGDDSRRKTGmTFDAQPGRKPGI 250
                                  |  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      
                                  1-MSE                       30-MSE                                                                        109-MSE     121-MSE  130-MSE                                      175-MSE                   201-MSE             221-MSE  |       238-MSE        
                                                                                                                                                                                                               176-MSE                                             228-MSE                  


Chain B from PDB  Type:PROTEIN  Length:256
 aligned with YCIK_ECOLI | P31808 from UniProtKB/Swiss-Prot  Length:252

    Alignment length:256
                                  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      
           YCIK_ECOLI     - ------MHYQPKQDLLNDRIILVTGASDGIGREAAMTYARYGATVILLGRNEEKLRQVASHINEETGRQPQWFILDLLTCTSENCQQLAQRIAVNYPRLDGVLHNAGLLGDVCPMSEQNPQVWQDVMQVNVNATFMLTQALLPLLLKSDAGSLVFTSSSVGRQGRANWGAYAASKFATEGMMQVLADEYQQRLRVNCINPGGTRTAMRASAFPTEDPQKLKTPADIMPLYLWLMGDDSRRKTGMTFDAQPGRKPGI 250
               SCOP domains d3e9qb_ B: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3e9qB00 B:-5-250 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhhh....eee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhh.....eee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:152-180    ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e9q B  -5 NLYFQGmHYQPKQDLLNDRIILVTGASDGIGREAAmTYARYGATVILLGRNEEKLRQVASHINEETGRQPQWFILDLLTCTSENCQQLAQRIVVNYPRLDGVLHNAGLLGDVCPmSEQNPQVWQDVmQINVNATFmLTQALLPLLLKSDAGSLVFTSSSVGRQGRANWGAYAASKFATEGmmQVLADEYQQRLRVNCINPGGTRTAmRASAFPTEDPQKLKTPADImPLYLWLmGDDSRRKTGmTFDAQPGRKPGI 250
                                  |  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      
                                  1-MSE                       30-MSE                                                                        109-MSE     121-MSE  130-MSE                                      175-MSE                   201-MSE             221-MSE  |       238-MSE        
                                                                                                                                                                                                               176-MSE                                             228-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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E9Q)

(-) Gene Ontology  (3, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q83RM3_SHIFL | Q83RM3)
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.

Chain A,B   (YCIK_ECOLI | P31808)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        YCIK_ECOLI | P31808: 3f1k 3f1l
UniProtKB/TrEMBL
        Q83RM3_SHIFL | Q83RM3: 3f5s 3gy0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3E9Q)