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(-) Description

Title :  CRYSTAL STRUCTURE OF ENOLASE MSMEG_6132 (TARGET EFI-502282) FROM MYCOBACTERIUM SMEGMATIS STR. MC2 155 COMPLEXED WITH TARTRATE
 
Authors :  Y. Patskovsky, R. Toro, R. Bhosle, B. Hillerich, R. D. Seidel, E. Washin A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, W. D. Zencheck, H J. A. Gerlt, S. C. Almo, Enzyme Function Initiative (Efi)
Date :  09 Jan 12  (Deposition) - 25 Jan 12  (Release) - 07 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Enolase, Magnesium Binding Site, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, R. Bhosle, B. Hillerich, R. D. Seidel, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, W. D. Zencheck, H. J. Imker, J. A. Gerlt, S. C. Almo
Crystal Structure Of Enolase Msmeg_6132 From Mycobacterium Smegmatis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE GLUCARATE DEHYDRATASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MSMEG_6132
    Organism Scientific: MYCOBACTERIUM SMEGMATIS STR. MC2 155
    Organism Taxid: 246196
    Strain: ATCC 700084 / MC(2)155

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3TLA1Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3TLA2Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:25 , HIS A:30 , TYR A:150 , LYS A:194 , ASN A:224 , HIS A:321 , SER A:322 , ASN A:323 , HIS A:350 , ARG A:403 , HOH A:754 , HOH A:755 , HOH A:756 , HOH A:769 , HOH A:770BINDING SITE FOR RESIDUE TLA A 501
2AC2SOFTWAREALA A:101 , PRO A:251 , GLY A:252 , MET A:271 , CYS A:272 , HOH A:628BINDING SITE FOR RESIDUE DTT A 502
3AC3SOFTWAREARG A:5 , ARG A:73 , SER A:74 , GLY A:415BINDING SITE FOR RESIDUE CL A 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:420 -Pro A:421

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VFC)

(-) Exons   (0, 0)

(no "Exon" information available for 3VFC)

(-) 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:417
 aligned with A0R5B5_MYCS2 | A0R5B5 from UniProtKB/TrEMBL  Length:423

    Alignment length:424
                             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    
         A0R5B5_MYCS2     - -MAHNRIRITGARVTPVAFADPPLLNTVGVHQPYALRAVIQLDTDAGLTGLGETYADTVHLERLQAAAHAIVGRSVFSTNVIRALISDALGGDRTGDGSGLAGMITSASVVDRVFSPFEVACLDVQGQVTGRPVSDLLGGAVRDAVPFSAYLFYKWAAHPGAEPDGWGAALDPDGIVAQARRMIDEYGFSAIKLKGGVFAPEEEMAAVEALRAAFPDHPLRLDPNAAWTPQTSVKVAAGLEGVLEYLEDPTPGLDGMAEVAAQAPMPLATNMCVVAFDQLPAAVAKNSVQVVLSDHHYWGGLQRSRLLAGICDTFGLGLSMHSNSHLGISLAAMVHLAAATPNLTYACDTHWPWRHEDVVAPGALNFCDGEVQVPATPGLGVEIDEDALAALHEQYLRCGIRDRDDTGYMRSIDPGFNASGPRW 423
               SCOP domains d3vfca1 A:0-138 automated matches                                                                                                          d3vfca2 A:139-423 automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeeeeeeeeeee....ee..ee...eeeeeeeeeee....eeeeee..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...-------....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee..eeee..................hhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh.....eee....hhhhhhhhhhhh...eee.....hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh..........hhhhh...........ee..eee...........hhhhhhhhhhhhhhhh....hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vfc A   0 SMAHNRIRITGARVTPVAFADPPLLNTVGVHQPYALRAVIQLDTDAGLTGLGETYADTVHLERLQAAAHAIVGRSVFSTNVIRALISDALGGDR-------AGMITSASVVDRVFSPFEVACLDVQGQVTGRPVSDLLGGAVRDAVPFSAYLFYKWAAHPGAEPDGWGAALDPDGIVAQARRMIDEYGFSAIKLKGGVFAPEEEMAAVEALRAAFPDHPLRLDPNAAWTPQTSVKVAAGLEGVLEYLEDPTPGLDGMAEVAAQAPMPLATNMCVVAFDQLPAAVAKNSVQVVLSDHHYWGGLQRSRLLAGICDTFGLGLSMHSNSHLGISLAAMVHLAAATPNLTYACDTHWPWRHEDVVAPGALNFCDGEVQVPATPGLGVEIDEDALAALHEQYLRCGIRDRDDTGYMRSIDPGFNASGPRW 423
                                     9        19        29        39        49        59        69        79        89   |     - |     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    
                                                                                                                        93     101
   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, 2)

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 3VFC)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (A0R5B5_MYCS2 | A0R5B5)
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:0008872    glucarate dehydratase activity    Catalysis of the reaction: D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H2O.
    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: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/TrEMBL
        A0R5B5_MYCS2 | A0R5B5: 3vdg

(-) Related Entries Specified in the PDB File

3vdg STRUCTURE OF ENOLASE MSMEG_6132 COMPLEXED WITH FORMATE RELATED ID: EFI-502282 RELATED DB: TARGETTRACK