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(-) Description

Title :  CRYSTAL STRUCTURE OF A MEMBER OF ENOLASE SUPERFAMILY FROM BURKHOLDERIA PSEUDOMALLEI K96243
 
Authors :  Y. Patskovsky, J. Bonanno, J. M. Sauder, J. M. Gilmore, M. Iizuka, S. Ozy S. R. Wasserman, D. Smith, J. Gerlt, S. K. Burley, S. C. Almo, New York Research Center For Structural Genomics (Nysgxrc)
Date :  26 Apr 07  (Deposition) - 05 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Enolase, Racemase, Structural Genomics, Psi, Protein Structure Initiative, Nysgrc, New York Structural Genomics Research Consortium, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, J. Bonanno, J. M. Sauder, J. M. Gilmore, M. Iizuka, M. Gheyi, S. Ozyurt, S. R. Wasserman, D. Smith, J. Gerlt, S. K. Burley, S. C. Almo
Crystal Structure Of A Member Of Enolase Superfamily From Burkholderia Pseudomallei.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MANDELATE RACEMASE / MUCONATE LACTONIZING ENZYME
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Taxid: 562
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: BPSS2072
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 272560
    Strain: K96243

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 64)
No.NameCountTypeFull Name
1MSE64Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:174 , GLU A:218 , GLU A:244 , GLU A:270 , HIS A:320BINDING SITE FOR RESIDUE NA A 409
2AC2SOFTWARELYS B:174 , GLU B:218 , GLU B:244 , GLU B:270 , HIS B:320BINDING SITE FOR RESIDUE NA B 409

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:268 -Ser A:269
2Ala B:268 -Ser B:269

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2POD)

(-) 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:379
 aligned with Q63IJ7_BURPS | Q63IJ7 from UniProtKB/TrEMBL  Length:400

    Alignment length:398
                             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        
         Q63IJ7_BURPS     - -MKITEIETLRPEEFPNLLWVLVHTDEGITGLGETFYGACSAEAYIHEWAANRLIGEDPLQIDRHAKRLSGYLGFRSAGAEMRGNSALDIALWDIFGKATGQPIYQLLGGKCRDTIRTYNTCAGPHYVRTAKQQSVANWGLANSVSARYDDLNAFLHRADELALDLLDSGITAMKIWPFDPYAEASDGYYISKSDLKRALEPFEKIRRAVGDKMDVMVEFHSLWNLPPALQIAEALREYETFWHEDPIRMDSLSSLKRYAERSLAPVCASETLATRWGFRDLLETNAAGIVMLDISWCGGLSEARKIASMAEAWHLPVAPHDCTGPVVLTASTHLSLNAPNALVQESVRAFYDGWYRDLVTALPTVKDGHITVPDGPGLGLELMPDIRERLTIAVRNT 397
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------2podA02 A:101-377 Enolase                    superfamily                                                                                                                                                                                                                             -------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.....eeeeeeee....eeeeeee.hhhhhhhhhhhhhhhhhh.....hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.......eeeeee......-------------------...hhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhheeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhh....eee....hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhhh.....eeehhhhhh...........eee..eee.............hhhhhh.eeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pod A   0 SLKITEIETLRPEEFPNLLWVLVHTDEGITGLGETFYGACSAEAYIHEWAANRLIGEDPLQIDRHAKRLSGYLGFRSAGAEmRGNSALDIALWDIFGKATGQPIYQLLGGKCRDTIRTYNTCAGPHY-------------------ARYDDLNAFLHRADELALDLLDSGITAmKIWPFDPYAEASDGYYISKSDLKRALEPFEKIRRAVGDKmDVmVEFHSLWNLPPALQIAEALREYETFWHEDPIRmDSLSSLKRYAERSLAPVCASETLATRWGFRDLLETNAAGIVmLDISWCGGLSEARKIASmAEAWHLPVAPHDCTGPVVLTASTHLSLNAPNALVQESVRAFYDGWYRDLVTALPTVKDGHITVPDGPGLGLELmPDIRERLTIAVRNT 397
                                     9        19        29        39        49        59        69        79 |      89        99       109       119      |  -         -      |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        
                                                                                                            81-MSE                                      126                 146                        173-MSE                                 213-MSE                             249-MSE                                   291-MSE           309-MSE                                                                   383-MSE          
                                                                                                                                                                                                                                                  216-MSE                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:380
 aligned with Q63IJ7_BURPS | Q63IJ7 from UniProtKB/TrEMBL  Length:400

    Alignment length:400
                             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
         Q63IJ7_BURPS     - -MKITEIETLRPEEFPNLLWVLVHTDEGITGLGETFYGACSAEAYIHEWAANRLIGEDPLQIDRHAKRLSGYLGFRSAGAEMRGNSALDIALWDIFGKATGQPIYQLLGGKCRDTIRTYNTCAGPHYVRTAKQQSVANWGLANSVSARYDDLNAFLHRADELALDLLDSGITAMKIWPFDPYAEASDGYYISKSDLKRALEPFEKIRRAVGDKMDVMVEFHSLWNLPPALQIAEALREYETFWHEDPIRMDSLSSLKRYAERSLAPVCASETLATRWGFRDLLETNAAGIVMLDISWCGGLSEARKIASMAEAWHLPVAPHDCTGPVVLTASTHLSLNAPNALVQESVRAFYDGWYRDLVTALPTVKDGHITVPDGPGLGLELMPDIRERLTIAVRNTSD 399
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------2podB02 B:101-377 Enolase                     superfamily                                                                                                                                                                                                                            ---------------------- CATH domains
           Pfam domains (1) -------------MR_MLE_N-2podB01 B:13-108                                                                       --------------------------------------------------------------------------------------------MR_MLE-2podB03 B:201-269                                             ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------MR_MLE_N-2podB02 B:13-108                                                                       --------------------------------------------------------------------------------------------MR_MLE-2podB04 B:201-269                                             ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE_C-2podB05 B:269-381                                                                                       ------------------ Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MR_MLE_C-2podB06 B:269-381                                                                                       ------------------ Pfam domains (4)
         Sec.struct. author ...eeeeeeeee.....eeeeeeee....eeeeeee.hhhhhhhhhhhhhhhhhh.....hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.......eeeeee......--------------------..hhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhheeeee.....hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh...eee....hhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhhh.....eeehhhhhh...........eee..eee.............hhhhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pod B   0 SLKITEIETLRPEEFPNLLWVLVHTDEGITGLGETFYGACSAEAYIHEWAANRLIGEDPLQIDRHAKRLSGYLGFRSAGAEmRGNSALDIALWDIFGKATGQPIYQLLGGKCRDTIRTYNTCAGPHY--------------------RYDDLNAFLHRADELALDLLDSGITAmKIWPFDPYAEASDGYYISKSDLKRALEPFEKIRRAVGDKmDVmVEFHSLWNLPPALQIAEALREYETFWHEDPIRmDSLSSLKRYAERSLAPVCASETLATRWGFRDLLETNAAGIVmLDISWCGGLSEARKIASmAEAWHLPVAPHDCTGPVVLTASTHLSLNAPNALVQESVRAFYDGWYRDLVTALPTVKDGHITVPDGPGLGLELmPDIRERLTIAVRNTSD 399
                                     9        19        29        39        49        59        69        79 |      89        99       109       119      |  -         -       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
                                                                                                            81-MSE                                      126                  147                       173-MSE                                 213-MSE                             249-MSE                                   291-MSE           309-MSE                                                                   383-MSE            
                                                                                                                                                                                                                                                  216-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  (0, 0)

(no "SCOP Domain" information available for 2POD)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: Enolase_N (69)
(-)
Clan: Enolase_TIM (82)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q63IJ7_BURPS | Q63IJ7)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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.

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