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(-) Description

Title :  CRYSTAL STRUCTURE OF DIVERGENT ENOLASE FROM OCEANOBACILLUS IHEYENSIS COMPLEXED WITH MG
 
Authors :  A. A. Fedorov, E. V. Fedorov, J. M. Sauder, S. K. Burley, J. A. Gerlt, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  23 Jan 09  (Deposition) - 03 Feb 09  (Release) - 22 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (4x)
Keywords :  Divergent Enolase, Nysgxrc, Target 9375A, Isomerase, Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. F. Rakus, C. Kalyanaraman, A. A. Fedorov, E. V. Fedorov, F. P. Mills-Groninger, R. Toro, J. Bonanno, K. Bain, J. M. Sauder, S. K. Burley, S. C. Almo, M. P. Jacobson, J. A. Gerlt
Computation-Facilitated Assignment Of The Function In The Enolase Superfamily: A Regiochemically Distinct Galactarate Dehydratase From Oceanobacillus Iheyensis .
Biochemistry V. 48 11546 2009
PubMed-ID: 19883118  |  Reference-DOI: 10.1021/BI901731C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MUCONATE CYCLOISOMERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: OB2843
    Organism Scientific: OCEANOBACILLUS IHEYENSIS HTE831
    Organism Taxid: 221109
    Strain: DSM 14371, JCM 11309, KCTC 3954, HTE831

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:193 , GLU A:221 , HIS A:246 , HOH A:557 , HOH A:565BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREASP A:42 , HIS A:45 , THR A:297 , HOH A:631 , HOH A:632BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWAREASP B:193 , GLU B:221 , HIS B:246 , HOH B:411 , HOH B:630BINDING SITE FOR RESIDUE MG B 401
4AC4SOFTWAREASP B:42 , HIS B:45 , THR B:297 , HOH B:633 , HOH B:634BINDING SITE FOR RESIDUE MG B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:46 -Pro A:47
2Leu B:46 -Pro B:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FYY)

(-) 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:375
 aligned with GALRD_OCEIH | Q8EMJ9 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:375
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370     
          GALRD_OCEIH     1 MKITDLELHAVGIPRHTGFVNKHVIVKIHTDEGLTGIGEMSDFSHLPLYSVDLHDLKQGLLSILLGQNPFDLMKINKELTDNFPETMYYYEKGSFIRNGIDNALHDLCAKYLDISVSDFLGGRVKEKIKVCYPIFRHRFSEEVESNLDVVRQKLEQGFDVFRLYVGKNLDADEEFLSRVKEEFGSRVRIKSYDFSHLLNWKDAHRAIKRLTKYDLGLEMIESPAPRNDFDGLYQLRLKTDYPISEHVWSFKQQQEMIKKDAIDIFNISPVFIGGLTSAKKAAYAAEVASKDVVLGTTQELSVGTAAMAHLGCSLTNINHTSDPTGPELYVGDVVKNRVTYKDGYLYAPDRSVKGLGIELDESLLAKYQVPDLSWD 375
               SCOP domains d3fyya1 A:1-122 automated matches                                                                                         d3fyya2 A:123-375 automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeeeeeeeee....eeeeee...........hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee..eee....hhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhh.......eee......hhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...........hhhhhh..........ee..eee.............hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fyy A   1 MKITDLELHAVGIPRHTGFVNKHVIVKIHTDEGLTGIGEMSDFSHLPLYSVDLHDLKQGLLSILLGQNPFDLMKINKELTDNFPETMYYYEKGSFIRNGIDNALHDLCAKYLDISVSDFLGGRVKEKIKVCYPIFRHRFSEEVESNLDVVRQKLEQGFDVFRLYVGKNLDADEEFLSRVKEEFGSRVRIKSYDFSHLLNWKDAHRAIKRLTKYDLGLEMIESPAPRNDFDGLYQLRLKTDYPISEHVWSFKQQQEMIKKDAIDIFNISPVFIGGLTSAKKAAYAAEVASKDVVLGTTQELSVGTAAMAHLGCSLTNINHTSDPTGPELYVGDVVKNRVTYKDGYLYAPDRSVKGLGIELDESLLAKYQVPDLSWD 375
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370     


Chain B from PDB  Type:PROTEIN  Length:375
 aligned with GALRD_OCEIH | Q8EMJ9 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:375
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370     
          GALRD_OCEIH     1 MKITDLELHAVGIPRHTGFVNKHVIVKIHTDEGLTGIGEMSDFSHLPLYSVDLHDLKQGLLSILLGQNPFDLMKINKELTDNFPETMYYYEKGSFIRNGIDNALHDLCAKYLDISVSDFLGGRVKEKIKVCYPIFRHRFSEEVESNLDVVRQKLEQGFDVFRLYVGKNLDADEEFLSRVKEEFGSRVRIKSYDFSHLLNWKDAHRAIKRLTKYDLGLEMIESPAPRNDFDGLYQLRLKTDYPISEHVWSFKQQQEMIKKDAIDIFNISPVFIGGLTSAKKAAYAAEVASKDVVLGTTQELSVGTAAMAHLGCSLTNINHTSDPTGPELYVGDVVKNRVTYKDGYLYAPDRSVKGLGIELDESLLAKYQVPDLSWD 375
               SCOP domains d3fyyb1 B:1-122 automated matches                                                                                         d3fyyb2 B:123-375 automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeeeeeeeee....eeeeee...........hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh......eee..eee....hhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhheeeeee.....hhhhhhhhhhhhh.......eee......hhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...........hhhhhh..............eee.............hhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fyy B   1 MKITDLELHAVGIPRHTGFVNKHVIVKIHTDEGLTGIGEMSDFSHLPLYSVDLHDLKQGLLSILLGQNPFDLMKINKELTDNFPETMYYYEKGSFIRNGIDNALHDLCAKYLDISVSDFLGGRVKEKIKVCYPIFRHRFSEEVESNLDVVRQKLEQGFDVFRLYVGKNLDADEEFLSRVKEEFGSRVRIKSYDFSHLLNWKDAHRAIKRLTKYDLGLEMIESPAPRNDFDGLYQLRLKTDYPISEHVWSFKQQQEMIKKDAIDIFNISPVFIGGLTSAKKAAYAAEVASKDVVLGTTQELSVGTAAMAHLGCSLTNINHTSDPTGPELYVGDVVKNRVTYKDGYLYAPDRSVKGLGIELDESLLAKYQVPDLSWD 375
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370
   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  (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 3FYY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GALRD_OCEIH | Q8EMJ9)
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

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

UniProtKB/Swiss-Prot
        GALRD_OCEIH | Q8EMJ9: 2oqy 3es7 3es8 3gd6 3hpf

(-) Related Entries Specified in the PDB File

2oqy THE SAME PROTEIN CRYSTALLIZED IN DIFFERENT SPACE GROUP
3es7 THE SAME PROTEIN COMPLEXED WITH MG AND L-MALATE
3es8 THE SAME PROTEIN COMPLEXED WITH MG AND L-MALATE, DIFFERENT SPACE GROUP RELATED ID: NYSGXRC-9375A RELATED DB: TARGETDB