1MCZ Lyase date Aug 06, 2002
title Benzoylformate Decarboxylase From Pseudomonas Putida Complex Inhibitor, R-Mandelate
authors E.S.Polovnikova, A.K.Bera, M.S.Hasson
compound source
Molecule: Benzoylformate Decarboxylase
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Synonym: Bfd, Bfdc
Engineered: Yes
Organism_scientific: Pseudomonas Putida
Organism_taxid: 303
Gene: Mdlc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm105
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pkk233-2
symmetry Space Group: P 1 21 1
R_factor 0.200 R_Free 0.220
length a length b length c angle alpha angle beta angle gamma
134.800 209.600 163.400 90.00 97.10 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand MG, RMN, TDP, TPP enzyme Lyase E.C. BRENDA
related structures by homologous chain: 1BFD
F, N, K, E, M, C, L, A, J, O, P, B, H, D, I, G

Primary referenceStructural and kinetic analysis of catalysis by a thiamin diphosphate-dependent enzyme, benzoylformate decarboxylase., Polovnikova ES, McLeish MJ, Sergienko EA, Burgner JT, Anderson NL, Bera AK, Jordan F, Kenyon GL, Hasson MS, Biochemistry 2003 Feb 25;42(7):1820-30. PMID:12590569
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1305 Kb) [Save to disk]
  • Biological Unit Coordinates (1mcz.pdb1.gz) 329 Kb
  • Biological Unit Coordinates (1mcz.pdb2.gz) 330 Kb
  • Biological Unit Coordinates (1mcz.pdb3.gz) 329 Kb
  • Biological Unit Coordinates (1mcz.pdb4.gz) 330 Kb
  • LPC: Ligand-Protein Contacts for 1MCZ
  • CSU: Contacts of Structural Units for 1MCZ
  • Likely Quarternary Molecular Structure file(s) for 1MCZ
  • Structure Factors (2306 Kb)
  • Retrieve 1MCZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1MCZ from S2C, [Save to disk]
  • Re-refined 1mcz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1MCZ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1MCZ
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1MCZ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1mcza1, region A:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mcza2, region A:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mcza3, region A:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mczb1, region B:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mczb2, region B:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mczb3, region B:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mczc1, region C:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mczc2, region C:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mczc3, region C:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mczd1, region D:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mczd2, region D:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mczd3, region D:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mcze1, region E:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mcze2, region E:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mcze3, region E:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mczf1, region F:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mczf2, region F:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mczf3, region F:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mczg1, region G:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mczg2, region G:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mczg3, region G:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mczh1, region H:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mczh2, region H:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mczh3, region H:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mczi1, region I:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mczi2, region I:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mczi3, region I:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mczj1, region J:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mczj2, region J:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mczj3, region J:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mczk1, region K:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mczk2, region K:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mczk3, region K:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mczl1, region L:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mczl2, region L:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mczl3, region L:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mczm1, region M:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mczm2, region M:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mczm3, region M:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mczn1, region N:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mczn2, region N:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mczn3, region N:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mczo1, region O:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mczo2, region O:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mczo3, region O:342-525 [Jmol] [rasmolscript] [script source]
        - Domain d1mczp1, region P:182-341 [Jmol] [rasmolscript] [script source]
        - Domain d1mczp2, region P:2-181 [Jmol] [rasmolscript] [script source]
        - Domain d1mczp3, region P:342-525 [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1mcz_C] [1mcz_F] [1mcz] [1mcz_L] [1mcz_B] [1mcz_H] [1mcz_O] [1mcz_I] [1mcz_K] [1mcz_A] [1mcz_E] [1mcz_G] [1mcz_N] [1mcz_P] [1mcz_M] [1mcz_J] [1mcz_D]
  • SWISS-PROT database: [P20906]
  • Domain organization of [MDLC_PSEPU] by SWISSPFAM
  • Other resources with information on 1MCZ
  • Community annotation for 1MCZ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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