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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MUTANT E234A OF GALACTURONATE DEHYDRATASE FROM GEOBACILLUS SP. COMPLEXED WITH MG
 
Authors :  A. A. Fedorov, E. V. Fedorov, F. Groninger-Poe, J. A. Gerlt, S. C. Almo
Date :  16 Dec 11  (Deposition) - 19 Dec 12  (Release) - 19 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Enolase Fold, Galacturonate Dehydratase, Double Mg Site, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V. Fedorov, F. Groninger-Poe, J. A. Gerlt, S. C. Almo
Crystal Structure Of The Mutant E234A Of Galacturonate Dehydratase From Geobacillus Sp. Complexed With Mg
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MANDELATE RACEMASE/MUCONATE LACTONIZING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GYMC10_3367
    Mutation: YES
    Organism Scientific: PAENIBACILLUS SP.
    Organism Taxid: 481743
    Strain: Y412MC10

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:207 , GLU A:233 , GLU A:263 , HOH A:455 , HOH A:557 , HOH A:640BINDING SITE FOR RESIDUE MG A 393
2AC2SOFTWAREGLU A:238 , ASP A:261 , HOH A:690 , HOH A:691 , HOH A:692 , HOH A:693BINDING SITE FOR RESIDUE MG A 394
3AC3SOFTWAREGLY A:264 , LEU A:265 , TRP A:288 , HOH A:680 , HOH A:722 , HOH A:745 , HOH A:756BINDING SITE FOR RESIDUE EPE A 395

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V5F)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:288 -Pro A:289

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V5F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V5F)

(-) Exons   (0, 0)

(no "Exon" information available for 3V5F)

(-) Sequences/Alignments

Asymmetric/Biological 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:386
 aligned with D3EID5_GEOS4 | D3EID5 from UniProtKB/TrEMBL  Length:382

    Alignment length:386
                             1                                                                                                                                                                                                                                                                                                                                                                                          382   
                             |       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  |   
         D3EID5_GEOS4     - -MNITGIQSDWKVEKIEFAKLTGERARSAGANGRIGVHGKSCTVDIARITIDGQTGYGSSIHMTPEWAEDVIGRRLLDLFDDRGRLREAYRLQLEYPVLDWLGQRQGKPVYDLVSGAHLETGASLVVPCYDTSLYFDDLHLADERAAVALMQEEAMQGYAKGQRHFKIKVGRGGRHMPLWEGTKRDIAIVRGISEVAGPAGKIMIDANNAYNLNLTKEVLAALSDVNLYWLEEAFHEDEALYEDLKEWLGQRGQNVLIADGEGLASPHLIEWATRGRVDVLQYDIIWPGFTHWMELGEKLDAHGLRSAPHCYGNAYGIYASGHLSAAVRNFEFVEYDDITIEGMDVSGYRIENGEIHVPATPGFGIVFDDELVTYLINRSGWS---   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeeeeeeeeee.........eeeeeeeeeeeee..eeeeee....hhhhhhhhh..hhhh.ee...ee...hhhhhhhhhhhhhhhhhh.hhhhhh..........eeeeeeeeee........hhhhhhhhhhhhhhhhhhh....eeee.hhhhh..hhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhh...eeee.......hhhhhhhh....ee.......hhhhhhhhhhhhhhh..ee......hhhhhhhhhhhh........eee..eee..ee....eee..eeee........eehhhhhhhhhhhh.eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3v5f A   2 SLNITGIQSDWKVEKIEFAKLTGERARSAGANGRIGVHGKSCTVDIARITIDGQTGYGSSIHMTPEWAEDVIGRRLLDLFDDRGRLREAYRLQLEYPVLDWLGQRQGKPVYDLVSGAHLETGASLVVPCYDTSLYFDDLHLADERAAVALMQEEAMQGYAKGQRHFKIKVGRGGRHMPLWEGTKRDIAIVRGISEVAGPAGKIMIDANNAYNLNLTKEVLAALSDVNLYWLEAAFHEDEALYEDLKEWLGQRGQNVLIADGEGLASPHLIEWATRGRVDVLQYDIIWPGFTHWMELGEKLDAHGLRSAPHCYGNAYGIYASGHLSAAVRNFEFVEYDDITIEGMDVSGYRIENGEIHVPATPGFGIVFDDELVTYLINRSGWSEGH 387
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381
   Legend:   → Mismatch (orange background)
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  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 3V5F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V5F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V5F)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D3EID5_GEOS4 | D3EID5)
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: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

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        D3EID5_GEOS4 | D3EID5: 3n4f 3ops 3p3b 3qpe 3v5c 3vcc

(-) Related Entries Specified in the PDB File

3p3b THE SAME WILD TYPE PROTEIN COMPLEXED WITH TARTRATE
3v5c