The Open Protein Structure Annotation Network
PDB Keyword


    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of putative cystathionine beta-lyase involved in aluminum resistance (NP_348457.1) from Clostridium acetobutylicum at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3hvy Target Id 390679
    Molecular Characteristics
    Source Clostridium acetobutylicum atcc 824
    Alias Ids TPS14598,NP_348457.1, 3.40.640.10, 85642 Molecular Weight 47668.01 Da.
    Residues 426 Isoelectric Point 5.26
    Sequence mleftkrslmnkyninervlelyeralndvekefkyydeireynqlkvlkafqeeriseshftnssgyg yndigrdsldrvyanifntesafvrphfvngthaigaalfgnlrpndtmmsicgmpydtlhdiigmdds kkvgslreygvkykmvdlkdgkvdintvkeelkkddsiklihiqrstgygwrkslriaeiaeiiksire vnenvivfvdncygefveekeptdvgadiiagsliknigggiattggyiagkeeyvtqatfrvtvpgig gecgstfgvmrslyeglfmaphvtieavkgavfcarimelagfdvlpkyndkrtdiiqaikfndekkli dfikgiqtaspvdsfvqceawdmpgyedkvimaagtfvqgasielsadapirepyigylqggltfdhak lgvlialsklim
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.00 Rfree 0.187
    Matthews' coefficent 2.58 Rfactor 0.145
    Waters 866 Solvent Content 52.26

    Ligand Information



    Protein Summary


    Pfam: This protein is in family Alum_res (PF06838).


    Protein NP_348457.1 is from CLOSTRIDIUM ACETOBUTYLICUM.  Sequence alignment indicates that this protein belong to Pfam 06838, aluminum resistance protein. Both FFAS and SSM alignment suggests that this target is a structural homolog to 1CS1, 1GC0, 1I43, 1N8P, 1E5E, 1QGN,  1I41,   1IBJ,   1Y4I, 2NMP and  2FQ6, which are cystathionine or methionine enzymes.  Slightly differing from other cystathinine synthases, protein NP_348457.1 consists of two domains.  Instead of constructing the first domain as in other cystathionine synthases, residues (1 to 77) in protein NP_348457.1 forms a very long helix following a small helix in the first domain for interface interaction instead of forming its own small domain as the small N-terminals domain in other cystathionine synthases. In current model, the first domain of NP_348457.1 should be the second domain in its structural homologues.   This target is also a structural homolog to other two JCSG targets: MG0383S and 3FD0 with highly conserved active site in the C-terminals domain for PLP binding.  In protein NP_34857.1, Lys 243 is involved in Schiff Base formation.  The other highly conserved residues for cystathionine synthase includes: Tyr 68, Asn 99, Gly 100, Thr 101, Tyr 126, Gln 182, Asp 217 and Tyr 220.  There is some density in the active site of protein NP_34857.1.  Phosphate ion is molded in the density in each subunit. The position of PO4 is identical to the PLP’s phosphate position in other two JCSG targets via superposing comparison. Protein NP_348457.1 exists as a tetramer in each asymmetric unit. Interfacing interaction calculation also predicts the biomolecule of this target as a tetramer.




    Figure 1. Protein  NP_348457.1 consists of two domains instead of 3 domains in

    other cystathionine synthases.





    Figure 2. The biomolecule of Protein NP_348457.1 is  a tetramer. 



    Figure 3. The N-terminals domain in its structural homologues (such as 1I41(cyan), 1QGN(magenta) and 2NMP(yellow)) becomes a very long helix in first domain of Protein NP_348457.1(green).



    Figure 4. The very long helix in the first domain of each NP_348457.1 subunit participates in tetramer construction instead of forming its own domain.




    Figure 5. In each conserved active site of this protein, a phosphate ion belonging to PLP is modeled near to Lys 243, which is for Schiff Base formation with PLP molecule.




    1.    Steegborn, C.,  Messerschmidt, A.,  Laber, B.,  Streber, W.,  Huber, R.,  Clausen, T.  (1999) The crystal structure of cystathionine gamma-synthase from Nicotiana tabacum reveals its substrate and reaction specificity.  J.Mol.Biol.   290: 983-996   
    2.     Steegborn, C.,  Laber, B.,  Messerschmidt, A.,  Huber, R.,  Clausen, T.  (2001) Crystal structures of cystathionine gamma-synthase inhibitor complexes rationalize the increased affinity of a novel inhibitor.  J.Mol.Biol.   311: 789-801   

    Ligand Summary




    No references found.

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