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(-) Description

Title :  CRYSTAL STRUCTURE OF MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME FROM BACILLUS SUBTILIS AT 1.8 A RESOLUTION
 
Authors :  V. N. Malashkevich, R. Toro, J. M. Sauder, K. D. Schwinn, S. Emtage, D. A. M. E. Rutter, M. Dickey, C. Groshong, K. T. Bain, J. M. Adams, C. Reyes, I A. Powell, A. Boice, T. Gheyi, S. Ozyurt, S. Atwell, S. R. Wasserman, S. A. Sali, P. Babbitt, U. Pieper, J. A. Gerlt, S. C. Almo, New York Sgx R Center For Structural Genomics (Nysgxrc)
Date :  16 Mar 06  (Deposition) - 04 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Mandelate Racemase/Muconate Lactonizing Enzyme, Tim-Barrel, Enolase, Octamer, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, R. Toro, J. M. Sauder, K. D. Schwinn, S. Emtage, D. A. Thompson, M. E. Rutter, M. Dickey, C. Groshong, K. T. Bain, J. M. Adams, C. Reyes, I. Rooney, A. Powell, A. Boice, T. Gheyi, S. Ozyurt, S. Atwell, S. R. Wasserman, S. K. Burley, A. Sali, P. Babbitt U. Pieper, J. A. Gerlt, S. C. Almo
Crystal Structure Of Mandelate Racemase/Muconate Lactonizin Enzyme From Bacillus Subtilis At 1. 8 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - YITF
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: MANDELATE RACEMASE/MUCONATE LACTONIZING ENZYME
    Gene: YITF
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2GDQ)

(-) Sites  (0, 0)

(no "Site" information available for 2GDQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GDQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GDQ)

(-) 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:373
 aligned with YITF_BACSU | O06741 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:373
                             1                                                                                                                                                                                                                                                                                                                                                                               371 
                             |       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 | 
           YITF_BACSU     - -MKIVRIETFPLFHRLEKPYGDANGFKRYRTCYLIRIITESGIDGWGECVDWLPALHVGFTKRIIPFLLGKQAGSRLSLVRTIQKWHQRAASAVSMALTEIAAKAADCSVCELWGGRYREEIPVYASFQSYSDSPQWISRSVSNVEAQLKKGFEQIKVKIGGTSFKEDVRHINALQHTAGSSITMILDANQSYDAAAAFKWERYFSEWTNIGWLEEPLPFDQPQDYAMLRSRLSVPVAGGENMKGPAQYVPLLSQRCLDIIQPDVMHVNGIDEFRDCLQLARYFGVRASAHAYDGSLSRLYALFAQACLPPWSKMKNDHIEPIEWDVMENPFTDLVSLQPSKGMVHIPKGKGIGTEINMEIVNRYKWDGSAY-   -
               SCOP domains -d2gdqa2 A:4-118 Hypothetical protein YitF                                                                          d2gdqa1 A:119-374 Hypothetical protein YitF                                                                                                                                                                                                                     - SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeee....eeeeee..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh......eeeeeee........hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh....eeeee......hhhhhhhhhh.....eee.....hhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhhh.ee.......hhhhhhhhhhhhh..............eeee...hhhhhhh.......eee...........hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gdq A   3 LVKIVRIETFPLFHRLEKPYGDANGFKRYRTCYLIRIITESGIDGWGECVDWLPALHVGFTKRIIPFLLGKQAGSRLSLVRTIQKWHQRAASAVSMALTEIAAKAADCSVCELWGGRYREEIPVYASFQSYSDSPQWISRSVSNVEAQLKKGFEQIKVKIGGTSFKEDVRHINALQHTAGSSITMILDANQSYDAAAAFKWERYFSEWTNIGWLEEPLPFDQPQDYAMLRSRLSVPVAGGENMKGPAQYVPLLSQRCLDIIQPDVMHVNGIDEFRDCLQLARYFGVRASAHAYDGSLSRLYALFAQACLPPWSKMKNDHIEPIEWDVMENPFTDLVSLQPSKGMVHIPKGKGIGTEINMEIVNRYKWDGSAYE 375
                                    12        22        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       282       292       302       312       322       332       342       352       362       372   


Chain B from PDB  Type:PROTEIN  Length:373
 aligned with YITF_BACSU | O06741 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:373
                             1                                                                                                                                                                                                                                                                                                                                                                               371 
                             |       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 | 
           YITF_BACSU     - -MKIVRIETFPLFHRLEKPYGDANGFKRYRTCYLIRIITESGIDGWGECVDWLPALHVGFTKRIIPFLLGKQAGSRLSLVRTIQKWHQRAASAVSMALTEIAAKAADCSVCELWGGRYREEIPVYASFQSYSDSPQWISRSVSNVEAQLKKGFEQIKVKIGGTSFKEDVRHINALQHTAGSSITMILDANQSYDAAAAFKWERYFSEWTNIGWLEEPLPFDQPQDYAMLRSRLSVPVAGGENMKGPAQYVPLLSQRCLDIIQPDVMHVNGIDEFRDCLQLARYFGVRASAHAYDGSLSRLYALFAQACLPPWSKMKNDHIEPIEWDVMENPFTDLVSLQPSKGMVHIPKGKGIGTEINMEIVNRYKWDGSAY-   -
               SCOP domains d2gdqb2 B:3-118 Hypothetical protein YitF                                                                           d2gdqb1 B:119-375 Hypothetical protein YitF                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeeeeeeeeee..eeeeeeeeeeeeeee....eeeeee..hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhh......eeeeeee........hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh....eeeee......hhhhhhhhhh.....eee.....hhhhhhhhhhh....ee........hhhhhhhhhhhhhhhh.ee.......hhhhhhhhhhhhh..............eeee...hhhhhh........eee...........hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gdq B   3 LVKIVRIETFPLFHRLEKPYGDANGFKRYRTCYLIRIITESGIDGWGECVDWLPALHVGFTKRIIPFLLGKQAGSRLSLVRTIQKWHQRAASAVSMALTEIAAKAADCSVCELWGGRYREEIPVYASFQSYSDSPQWISRSVSNVEAQLKKGFEQIKVKIGGTSFKEDVRHINALQHTAGSSITMILDANQSYDAAAAFKWERYFSEWTNIGWLEEPLPFDQPQDYAMLRSRLSVPVAGGENMKGPAQYVPLLSQRCLDIIQPDVMHVNGIDEFRDCLQLARYFGVRASAHAYDGSLSRLYALFAQACLPPWSKMKNDHIEPIEWDVMENPFTDLVSLQPSKGMVHIPKGKGIGTEINMEIVNRYKWDGSAYE 375
                                    12        22        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       282       292       302       312       322       332       342       352       362       372
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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 2GDQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (YITF_BACSU | O06741)
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:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        YITF_BACSU | O06741: 2gge

(-) Related Entries Specified in the PDB File

1muc MUCONATE LACTONIZING ENZYME
1yey L-FUCONATE DEHYDRATASE FROM 2 XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS STR. ATCC 33913 RELATED ID: NYSGXRC-9293A RELATED DB: TARGETDB