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(-) Description

Title :  CRYSTAL STRUCTURE OF A SHORT CHAIN DEHYDROGENASE FROM RHIZOBIUM ETLI CFN 42
 
Authors :  R. Agarwal, S. Chamala, B. Evans, R. Foti, A. Gizzi, B. Hillerich, A. Kar J. Lafleur, R. Siedel, G. Villigas, W. Zencheck, S. C. Almo, S. Swamina York Structural Genomics Research Consortium (Nysgrc)
Date :  16 Feb 12  (Deposition) - 29 Feb 12  (Release) - 29 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Agarwal, S. C. Almo, S. Swaminathan
Crystal Structure Of A Short Chain Dehydrogenase From Rhizobium Etli Cfn 42
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE OXIDOREDUCTASE PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RHE_PD00113
    Organism Scientific: RHIZOBIUM ETLI
    Organism Taxid: 347834
    Strain: CFN 42 / ATCC 51251
    Synonym: SHORT CHAIN DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 36)

Asymmetric/Biological Unit (1, 36)
No.NameCountTypeFull Name
1MSE36Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4DQX)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DQX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DQX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DQX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DQX)

(-) Exons   (0, 0)

(no "Exon" information available for 4DQX)

(-) 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 Q8KL31_RHIEC | Q8KL31 from UniProtKB/TrEMBL  Length:255

    Alignment length:255
                             1                                                                                                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249     
         Q8KL31_RHIEC     - -MDLNQRVCIVTGGGSGIGRATAELFAKNGAYVVVADVNEDAAVRVANEIGSKAFGVRVDVSSAKDAESMVEKTTAKWGRVDVLVNNAGFGTTGNVVTIPEETWDRIMSVNVKGIFLCSKYVIPVMRRNGGGSIINTTSYTATSAIADRTAYVASKGAISSLTRAMAMDHAKEGIRVNAVAPGTIDSPYFTKIFAEAKDPAKLRSDFNARAVMDRMGTAEEIAEAMLFLASDRSRFATGSILTVDGGSSIGNHLV 254
               SCOP domains d4dqxa_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dqx A  22 SmDLNQRVCIVTGGGSGIGRATAELFAKNGAYVVVADVNEDAAVRVANEIGSKAFGVRVDVSSAKDAESmVEKTTAKWGRVDVLVNNAGFGTTGNVVTIPEETWDRImSVNVKGIFLCSKYVIPVmRRNGGGSIINTTSYTATSAIADRTAYVASKGAISSLTRAmAmDHAKEGIRVNAVAPGTIDSPYFTKIFAEAKDPAKLRSDFNARAVmDRmGTAEEIAEAmLFLASDRSRFATGSILTVDGGSSIGNHLV 276
                             |      31        41        51        61        71        81        91       101       111       121       131       141     | 151       161       171       181     | 191       201       211       221       231  |  | 241     | 251       261       271     
                             |                                                                  91-MSE                               129-MSE           147-MSE                                 187-MSE                                        234-MSE      247-MSE                         
                            23-MSE                                                                                                                                                               189-MSE                                         237-MSE                                   


Chain B from PDB  Type:PROTEIN  Length:250
 aligned with Q8KL31_RHIEC | Q8KL31 from UniProtKB/TrEMBL  Length:255

    Alignment length:253
                                    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   
         Q8KL31_RHIEC     1 MDLNQRVCIVTGGGSGIGRATAELFAKNGAYVVVADVNEDAAVRVANEIGSKAFGVRVDVSSAKDAESMVEKTTAKWGRVDVLVNNAGFGTTGNVVTIPEETWDRIMSVNVKGIFLCSKYVIPVMRRNGGGSIINTTSYTATSAIADRTAYVASKGAISSLTRAMAMDHAKEGIRVNAVAPGTIDSPYFTKIFAEAKDPAKLRSDFNARAVMDRMGTAEEIAEAMLFLASDRSRFATGSILTVDGGSSIGNHL 253
               SCOP domains d4dqxb_ B: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhh---.hhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dqx B  23 mDLNQRVCIVTGGGSGIGRATAELFAKNGAYVVVADVNEDAAVRVANEIGSKAFGVRVDVSSAKDAESmVEKTTAKWGRVDVLVNNAGFGTTGNVVTIPEETWDRImSVNVKGIFLCSKYVIPVmRRNGGGSIINTTSYTATSAIADRTAYVASKGAISSLTRAmAmDHAKEGIRVNAVAPGTIDSPYFTKIFA---DPAKLRSDFNARAVmDRmGTAEEIAEAmLFLASDRSRFATGSILTVDGGSSIGNHL 275
                            |       32        42        52        62        72        82        92       102       112       122      |132       142    |  152       162       172       182    | |192       202       212   |   222       232 |  |  242    |  252       262       272   
                           23-MSE                                                              91-MSE                               129-MSE           147-MSE                                 187-MSE                      216 220           234-MSE      247-MSE                        
                                                                                                                                                                                                189-MSE                                         237-MSE                                  


Chain C from PDB  Type:PROTEIN  Length:251
 aligned with Q8KL31_RHIEC | Q8KL31 from UniProtKB/TrEMBL  Length:255

    Alignment length:256
                              1                                                                                                                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248      
         Q8KL31_RHIEC     - --MDLNQRVCIVTGGGSGIGRATAELFAKNGAYVVVADVNEDAAVRVANEIGSKAFGVRVDVSSAKDAESMVEKTTAKWGRVDVLVNNAGFGTTGNVVTIPEETWDRIMSVNVKGIFLCSKYVIPVMRRNGGGSIINTTSYTATSAIADRTAYVASKGAISSLTRAMAMDHAKEGIRVNAVAPGTIDSPYFTKIFAEAKDPAKLRSDFNARAVMDRMGTAEEIAEAMLFLASDRSRFATGSILTVDGGSSIGNHLV 254
               SCOP domains d4dqxc_ C: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhh-----.hhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dqx C  21 QSmDLNQRVCIVTGGGSGIGRATAELFAKNGAYVVVADVNEDAAVRVANEIGSKAFGVRVDVSSAKDAESmVEKTTAKWGRVDVLVNNAGFGTTGNVVTIPEETWDRImSVNVKGIFLCSKYVIPVmRRNGGGSIINTTSYTATSAIADRTAYVASKGAISSLTRAmAmDHAKEGIRVNAVAPGTIDSPYFTKIF-----PAKLRSDFNARAVmDRmGTAEEIAEAmLFLASDRSRFATGSILTVDGGSSIGNHLV 276
                              |     30        40        50        60        70        80        90|      100       110       120       130       140      |150       160       170       180      |190       200       210    |    -|      230   |  |240      |250       260       270      
                             23-MSE                                                              91-MSE                               129-MSE           147-MSE                                 187-MSE                     215   221          234-MSE      247-MSE                         
                                                                                                                                                                                                  189-MSE                                         237-MSE                                   


Chain D from PDB  Type:PROTEIN  Length:250
 aligned with Q8KL31_RHIEC | Q8KL31 from UniProtKB/TrEMBL  Length:255

    Alignment length:255
                              1                                                                                                                                                                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248     
         Q8KL31_RHIEC     - --MDLNQRVCIVTGGGSGIGRATAELFAKNGAYVVVADVNEDAAVRVANEIGSKAFGVRVDVSSAKDAESMVEKTTAKWGRVDVLVNNAGFGTTGNVVTIPEETWDRIMSVNVKGIFLCSKYVIPVMRRNGGGSIINTTSYTATSAIADRTAYVASKGAISSLTRAMAMDHAKEGIRVNAVAPGTIDSPYFTKIFAEAKDPAKLRSDFNARAVMDRMGTAEEIAEAMLFLASDRSRFATGSILTVDGGSSIGNHL 253
               SCOP domains d4dqxd_ D: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhh-----.hhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dqx D  21 QSmDLNQRVCIVTGGGSGIGRATAELFAKNGAYVVVADVNEDAAVRVANEIGSKAFGVRVDVSSAKDAESmVEKTTAKWGRVDVLVNNAGFGTTGNVVTIPEETWDRImSVNVKGIFLCSKYVIPVmRRNGGGSIINTTSYTATSAIADRTAYVASKGAISSLTRAmAmDHAKEGIRVNAVAPGTIDSPYFTKIFAE-----KLRSDFNARAVmDRmGTAEEIAEAmLFLASDRSRFATGSILTVDGGSSIGNHL 275
                              |     30        40        50        60        70        80        90|      100       110       120       130       140      |150       160       170       180      |190       200       210      |  -  |    230   |  |240      |250       260       270     
                             23-MSE                                                              91-MSE                               129-MSE           147-MSE                                 187-MSE                       217   223        234-MSE      247-MSE                        
                                                                                                                                                                                                  189-MSE                                         237-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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DQX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DQX)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q8KL31_RHIEC | Q8KL31)
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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