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(-) Description

Title :  CRYSTAL STRUCTURE OF ENOLASE MSMEG_6132 (TARGET EFI-502282) FROM MYCOBACTERIUM SMEGMATIS STR. MC2 155 COMPLEXED WITH FORMATE AND ACETATE
 
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 :  05 Jan 12  (Deposition) - 25 Jan 12  (Release) - 07 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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 Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    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  (4, 4)

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3FMT1Ligand/IonFORMIC ACID
4NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3FMT2Ligand/IonFORMIC ACID
4NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:194 , ASN A:224 , ASN A:270 , HIS A:321 , ASN A:323 , NA A:502 , ACT A:504 , HOH A:726 , HOH A:767 , HOH A:770 , HOH A:779BINDING SITE FOR RESIDUE FMT A 501
2AC2SOFTWARELYS A:192 , ASP A:222 , GLU A:247 , ASN A:270 , FMT A:501 , HOH A:603 , HOH A:767BINDING SITE FOR RESIDUE NA A 502
3AC3SOFTWAREARG A:5 , ARG A:73 , SER A:74 , GLY A:415 , HOH A:950BINDING SITE FOR RESIDUE CL A 503
4AC4SOFTWAREASN A:25 , HIS A:30 , LYS A:194 , HIS A:350 , ARG A:403 , FMT A:501 , HOH A:726 , HOH A:769 , HOH A:779BINDING SITE FOR RESIDUE ACT A 504

(-) SS Bonds  (0, 0)

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

(-) 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 3VDG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VDG)

(-) 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:424
 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 d3vdga1 A:0-138 automated matches                                                                                                          d3vdga2 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.................hhhhhhhhhhhhhhhhhhhhhhh.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
                 3vdg A   0 SMAHNRIRITGARVTPVAFADPPLLNTVGVHQPYALRAVIQLDTDAGLTGLGETYADTVHLERLQAAAHAIVGRSVFSTNVIRALISDALGGDRTGDGSGLAGMITSASVVDRVFSPFEVACLDVQGQVTGRPVSDLLGGAVRDAVPFSAYLFYKWAAHPGAEPDGWGAALDPDGIVAQARRMIDEYGFSAIKLKGGVFAPEEEMAAVEALRAAFPDHPLRLDPNAAWTPQTSVKVAAGLEGVLEYLEDPTPGLDGMAEVAAQAPMPLATNMCVVAFDQLPAAVAKNSVQVVLSDHHYWGGLQRSRLLAGICDTFGLGLSMHSNSHLGISLAAMVHLAAATPNLTYACDTHWPWRHEDVVAPGALNFCDGEVQVPATPGLGVEIDEDALAALHEQYLRCGIRDRDDTGYMRSIDPGFNASGPRW 423
                                     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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3VDG)

(-) Pfam Domains  (0, 0)

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

(-) 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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