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(-) Description

Title :  STRUCTURE OF [FES]CLUSTER-FREE APO FORM OF 6-PHOSPHOGLUCONATE DEHYDRATASE FROM SHEWANELLA ONEIDENSIS
 
Authors :  N. Schormann, J. Symersky, Southeast Collaboratory For Structura Genomics (Secsg)
Date :  16 Apr 06  (Deposition) - 09 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  N-Terminal Domain Largely Alpha-Helical, C-Terminal Domain Mainly Beta-Sheet (Trefoil-Like), Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Schormann, J. Symersky, E. Karpova, Y. Zhang, S. Lu, S. Qiu, R. Bunzel, C. -H. Luan, W. Huang, M. Luo, J. Tsao, D. Johnson, M. Carson, Q. Zhou, D. Luo, R. Gray, Z. Cao, J. An, A. Arabshahi, S. Li, M. Stinnett, A. Mckinstry, G. Lin, Q. Shang, Y. Chen, L. Delucas
Structure Of [Fes]Cluster-Free Apo Form Of 6-Phosphogluconate Dehydratase From Shewanella Oneidensis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 6-PHOSPHOGLUCONATE DEHYDRATASE
    Chains: A, B
    EC Number: 4.2.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EDD
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 211586
    Strain: MR-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 28)

Asymmetric Unit (1, 28)
No.NameCountTypeFull Name
1MSE28Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2GP4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GP4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Thr A:526 -Pro A:527
2Thr B:526 -Pro B:527

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GP4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GP4)

(-) Exons   (0, 0)

(no "Exon" information available for 2GP4)

(-) 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:523
 aligned with Q8EEA0_SHEON | Q8EEA0 from UniProtKB/TrEMBL  Length:608

    Alignment length:609
                             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       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599         
         Q8EEA0_SHEON     - -MHSVVQSVTDRIIARSKASREAYLAALNDARNHGVHRSSLSCGNLAHGFAACNPDDKNALRQLTKANIGIITAFNDMLSAHQPYETYPDLLKKACQEVGSVAQVAGGVPAMCDGVTQGQPGMELSLLSREVIAMATAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLFVPAGPMKSGIPNKEKARIRQQFAQGKVDRAQLLEAEAQSYHSAGTCTFYGTANSNQLMLEVMGLQLPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSIVNGIVALLATGGSTNLTMHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFLIKELLDAGLLHEDVNTVAGYGLRRYTQEPKLLDGELRWVDGPTVSLDTEVLTSVATPFQNNGGLKLLKGNLGRAVIKVSAVQPQHRVVEAPAVVIDDQNKLDALFKSGALDRDCVVVVKGQGPKANGMPELHKLTPLLGSLQDKGFKVALMTDGRMSGASGKVPAAIHLTPEAIDGGLIAKVQDGDLIRVDALTGELSLLVSDTELATRTATEIDLRHSRYGMGRELFGVLRSNLSSPETGARSTSAIDELY 608
               SCOP domains -d2gp4a2 A:1-418 6-phosphogluconat                                                        e d   ehydratase  ED  D                                                                                                                                                                                                                                                                                                                  d2gp4a1 A:419-608 6-phosphogluconate dehydratase EDD                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.--------------------------------------------------------...---....eeeee.-...--........hhhhhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhh.....eee.....-------------------..hhhhhhhhh...hhhhhhhhhhh.-----hhhhhhh.....hhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhh.......hhhhh..hhhhhhhhhhhhhhhhhhhhh.......ee..ee.hhhh.eeeeee..eeeeee.......................eeeeee..eeeeee....hhhh.eeeeeeeee.hhhhhhhhhhh......eeeee...hhhhhh......hhhhhhhhhhh...eeeee............eeeeee.hhhhhhhhhh.....eeeee....eeee..hhhhhhhh......hhhhh...hhhhhhhhhhh..hhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gp4 A   0 HmHSVVQSVTDRIIARSKASREAYLAALNDARNH--------------------------------------------------------LLK---QEVGSVAQVA-GVP--CDGVTQGQPGmELSLLSREVIAmATAVGLSHNmFDGALLLGICDKIVPGLLIGALSFGHLPmLFVPAGP-------------------GKVDRAQLLEAEAQSYHSAGTCTFYG-----QLmLEVmGLQLPGSSFVNPDDPLREALNKmAAKQVCRLTELGTQYSPIGEVVNEKSIVNGIVALLATGGSTNLTmHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGmAFLIKELLDAGLLHEDVNTVAGYGLRRYTQEPKLLDGELRWVDGPTVSLDTEVLTSVATPFQNNGGLKLLKGNLGRAVIKVSAVQPQHRVVEAPAVVIDDQNKLDALFKSGALDRDCVVVVKGQGPKANGmPELHKLTPLLGSLQDKGFKVALmTDGRmSGASGKVPAAIHLTPEAIDGGLIAKVQDGDLIRVDALTGELSLLVSDTELATRTATEIDLRHSRYGmGRELFGVLRSNLSSPETGARSTSAIDELY 608
                             |       9        19        29   |     -         -         -         -         -         -| |   | 99     | 109  |    119  |    129    |  139    |  149       159       169   |   179|        -         -|      209       219     |   - | |   239       249       259|      269       279       289       299     | 309       319       329       339       349   |   359       369       379       389       399       409       419       429       439       449       459       469       479    |  489       499       509  |    519       529       539       549       559       569       579       589       599         
                             |                              33                                                       90 |  96      105 | |  |       122-MSE     134-MSE   144-MSE                      173-MSE180                 200                      225   231 |   |                    260-MSE                                      305-MSE                                         353-MSE                                                                                                                            484-MSE                507-MSE|                                                                579-MSE                         
                             1-MSE                                                                                     92            107 |  |                                                                                                                      233-MSE                                                                                                                                                                                                                                                                                512-MSE                                                                                            
                                                                                                                                       109  |                                                                                                                          237-MSE                                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                          112                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:495
 aligned with Q8EEA0_SHEON | Q8EEA0 from UniProtKB/TrEMBL  Length:608

    Alignment length:609
                             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       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599         
         Q8EEA0_SHEON     - -MHSVVQSVTDRIIARSKASREAYLAALNDARNHGVHRSSLSCGNLAHGFAACNPDDKNALRQLTKANIGIITAFNDMLSAHQPYETYPDLLKKACQEVGSVAQVAGGVPAMCDGVTQGQPGMELSLLSREVIAMATAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLFVPAGPMKSGIPNKEKARIRQQFAQGKVDRAQLLEAEAQSYHSAGTCTFYGTANSNQLMLEVMGLQLPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSIVNGIVALLATGGSTNLTMHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFLIKELLDAGLLHEDVNTVAGYGLRRYTQEPKLLDGELRWVDGPTVSLDTEVLTSVATPFQNNGGLKLLKGNLGRAVIKVSAVQPQHRVVEAPAVVIDDQNKLDALFKSGALDRDCVVVVKGQGPKANGMPELHKLTPLLGSLQDKGFKVALMTDGRMSGASGKVPAAIHLTPEAIDGGLIAKVQDGDLIRVDALTGELSLLVSDTELATRTATEIDLRHSRYGMGRELFGVLRSNLSSPETGARSTSAIDELY 608
               SCOP domains d2gp4b2 B:0-418 6-phosphogluconate                                                            dehydratase   ED  D                                                                                                                                                                                                                                                                                                                  d2gp4b1 B:419-608 6-phosphogluconate dehydratase EDD                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----------------------------------------------------------.......eeeee.--..--........hhhhhhhhhhhhhhhhhhhhhh.....eeeee...-hhhhhhhhhhhh.....eee.....--------------------------------------------------hhhhhhh.............hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhh.......hhhhh..hhhhhhhhhhhhhhhhhhhhh.......ee..ee.hhhh.eeeeee..eeeeee.......................eeeeee..eeeeee....hhhh.eeeeeeeee.hhhhhhhhhhh......eeeee...hhhhhh......hhhhhhhhhh....eeeee............eeeeee.hhhhhhhhhhh....eeeee....eeee..hhhhhh........hhhhh...hhhhhhhhhh...hhhhh.....hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gp4 B   0 HmHSVVQSVTDRIIARSKASREAYLAALNDARNH-----------------------------------------------------------KACQEVGSVAQVA--VP--CDGVTQGQPGmELSLLSREVIAmATAVGLSHNmFDGALLLGIC-KIVPGLLIGALSFGHLPmLFVPAGP--------------------------------------------------QLmLEVmGLQLPGSSFVNPDDPLREALNKmAAKQVCRLTELGTQYSPIGEVVNEKSIVNGIVALLATGGSTNLTmHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGmAFLIKELLDAGLLHEDVNTVAGYGLRRYTQEPKLLDGELRWVDGPTVSLDTEVLTSVATPFQNNGGLKLLKGNLGRAVIKVSAVQPQHRVVEAPAVVIDDQNKLDALFKSGALDRDCVVVVKGQGPKANGmPELHKLTPLLGSLQDKGFKVALmTDGRmSGASGKVPAAIHLTPEAIDGGLIAKVQDGDLIRVDALTGELSLLVSDTELATRTATEIDLRHSRYGmGRELFGVLRSNLSSPETGARSTSAIDELY 608
                             |       9        19        29   |     -         -         -         -         -         -   |    99     | 109  |    119  |    129    |  139    |  149    | |159       169   |   179|        -         -         -         -         - | |   239       249       259|      269       279       289       299     | 309       319       329       339       349   |   359       369       379       389       399       409       419       429       439       449       459       469       479    |  489       499       509  |    519       529       539       549       559       569       579       589       599         
                             1-MSE                          33                                                          93         105  ||  |       122-MSE     134-MSE   144-MSE   154 |              173-MSE180                                                231 |   |                    260-MSE                                      305-MSE                                         353-MSE                                                                                                                            484-MSE                507-MSE|                                                                579-MSE                         
                                                                                                                                      108|  |                                         156                                                                          233-MSE                                                                                                                                                                                                                                                                                512-MSE                                                                                            
                                                                                                                                       109  |                                                                                                                          237-MSE                                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                          112
   Legend:   → Mismatch (orange background)
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  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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GP4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GP4)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8EEA0_SHEON | Q8EEA0)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0004456    phosphogluconate dehydratase activity    Catalysis of the reaction: 6-phospho-D-gluconate = 2-dehydro-3-deoxy-6-phospho-D-gluconate + H(2)O.
biological process
    GO:0009255    Entner-Doudoroff pathway through 6-phosphogluconate    A pathway that converts a carbohydrate to pyruvate and glyceraldehyde-3 phosphate by producing 6-phosphogluconate and then dehydrating it.
    GO:0009082    branched-chain amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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