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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE FROM MYCOBACTERIUM MARINUM
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  18 Jan 11  (Deposition) - 02 Feb 11  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Seattle Structural Genomics Center For Infectious Disease, Ssgcid, 2- Hydroxyhepta-2, 4-Diene-1, 7-Dioate Isomerase, Mycobacterium, Tuberculosis, Non-Pathogenic Species, Rv2993C Ortholog, Homoprotocatechuate Degradative Pathway, 2-Hydroxyhepta-2, 4- Dienedioate, 2-Oxohept-3-Enedioate, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - 2-HYDROXYHEPTA-2,4-DIENE-1,7-DIOATE ISOMERASE
    Chains: A
    EC Number: 5.3.3.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: AVA0421
    Gene: MMAR_1718
    Organism Scientific: MYCOBACTERIUM MARINUM
    Organism Taxid: 216594
    Strain: M

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2ZN2Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:117 , GLU A:119 , ASP A:148 , EDO A:268 , HOH A:412BINDING SITE FOR RESIDUE ZN A 266
2AC2SOFTWAREGLU A:20 , ASP A:22 , GLU A:187 , HIS A:199BINDING SITE FOR RESIDUE ZN A 267
3AC3SOFTWAREVAL A:66 , GLU A:117 , GLU A:119 , ARG A:152 , GLN A:155 , LYS A:165 , ZN A:266BINDING SITE FOR RESIDUE EDO A 268
4AC4SOFTWAREPRO A:175 , TRP A:176 , GLY A:253 , THR A:254 , HOH A:359BINDING SITE FOR RESIDUE EDO A 269
5AC5SOFTWARELYS A:129 , ASP A:130 , ASP A:168 , SER A:217 , ALA A:218 , VAL A:219 , LYS A:262 , HOH A:321 , HOH A:325BINDING SITE FOR RESIDUE EDO A 270

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:112 -Pro A:113
2Gly A:174 -Pro A:175

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QDF)

(-) 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:252
 aligned with B2HIH3_MYCMM | B2HIH3 from UniProtKB/TrEMBL  Length:265

    Alignment length:265
                             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     
         B2HIH3_MYCMM     - -MRLGRIASPDGVAFASIEGELDNPGAMTAREIAEHPFGTPNFTGRSWPLADVRLLAPILASKVVCVGKNYTDHIAEMGGQTGPTPADPVIFLKPNTAIVGPNVPIRLPANASPVHFEGELAIVIGRPCKDVSAAQAVDNILGYTIGNDVSARDQQKSDGQWTRAKGHDTFCPVGPWIVTDVDPADLELRTEVNGAVKQHARTSLMIHDVGAIVEWISAVMTLLPGDLILTGTPAGVGPIEDGDTVSITIEGIGTLTNPVVRKGK 264
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -DUF2437-3qdfA02 A:1-57                                   ----FAA_hydrol             ase-3qdfA01 A:62-260                                                                                                                                                            ---- Pfam domains
         Sec.struct. author ..eeeeeee..eeeeeeee....hhhh.eeeeeee......eeeeeeee.hhheee.......eeee.....-------------.....eeeehhh.ee.....eee......eee.eeeeeee.......hhhhhhh.eeeeeeee..eehhhhhhhh.hhhhhh....eeeeeeee...hhhh.eeeeee..eeeeeee.hhh..hhhhhhhhhhhhh......eee.......ee.....eeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qdf A   0 SMRLGRIASPDGVAFASIEGELDNPGAMTAREIAEHPFGTPNFTGRSWPLADVRLLAPILASKVVCVGKNYT-------------PADPVIFLKPNTAIVGPNVPIRLPANASPVHFEGELAIVIGRPCKDVSAAQAVDNILGYTIGNDVSARDQQKSDGQWTRAKGHDTFCPVGPWIVTDVDPADLELRTEVNGAVKQHARTSLMIHDVGAIVEWISAVMTLLPGDLILTGTPAGVGPIEDGDTVSITIEGIGTLTNPVVRKGK 264
                                     9        19        29        39        49        59        69 |       -     |  89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259     
                                                                                                  71            85
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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 3QDF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: FAH (11)
(-)
Clan: no clan defined [family: DUF2437] (2)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (B2HIH3_MYCMM | B2HIH3)
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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