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(-) Description

Title :  CRYSTAL STRUCTURE OF TETRAMERIC BIODEGRADATIVE THREONINE DEAMINASE (TDCB) FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH CMP AT 2.5A RESOLUTION (HEXAGONAL FORM)
 
Authors :  D. K. Simanshu, H. S. Savithri, M. R. N. Murthy
Date :  09 Apr 06  (Deposition) - 07 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Tdcb, Biodegradative Threonine Deaminase, Plp, Cmp, Threonine Dehydratase, L-Threonine Metabolism, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. K. Simanshu, H. S. Savithri, M. R. Murthy
Crystal Structures Of Salmonella Typhimurium Biodegradative Threonine Deaminase And Its Complex With Cmp Provide Structural Insights Into Ligand-Induced Oligomerization And Enzyme Activation.
J. Biol. Chem. V. 281 39630 2006
PubMed-ID: 17046821  |  Reference-DOI: 10.1074/JBC.M605721200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THREONINE DEHYDRATASE CATABOLIC
    ChainsA
    EC Number4.3.1.19
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSET C
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTDCB
    Organism ScientificSALMONELLA TYPHIMURIUM
    Organism Taxid602
    StrainIFO 12529
    SynonymTHREONINE DEAMINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1C5P1Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2LLP1Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1C5P4Ligand/IonCYTIDINE-5'-MONOPHOSPHATE
2LLP4Mod. Amino Acid2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
3NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:171BINDING SITE FOR RESIDUE NA A 401
2AC2SOFTWAREASN A:34 , ARG A:53 , THR A:54 , GLY A:55 , GLN A:88 , ALA A:116 , ASP A:119 , TYR A:120 , GLN A:275 , ARG A:276 , LYS A:278 , ASN A:314 , HOH A:412 , HOH A:424 , HOH A:425 , HOH A:441BINDING SITE FOR RESIDUE C5P A 400

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:118 -A:118

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GN2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GN2)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDRATASE_SER_THRPS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.TDCB_SALTY49-62  1A:49-62
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDRATASE_SER_THRPS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.TDCB_SALTY49-62  4A:49-62

(-) Exons   (0, 0)

(no "Exon" information available for 2GN2)

(-) 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:326
 aligned with TDCB_SALTY | P11954 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:326
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322      
           TDCB_SALTY     3 ITYDLPVAIEDILEAKKRLAGKIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGAFNKLSSLTEAEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVVLHGDNFNDTIAKVSEIVETEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVIVPIGGGGLIAGIAIAIKSINPTIKVIGVQAENVHGMAASYYTGEITTHRTTGTLADGCDVSRPGNLTYEIVRELVDDIVLVSEDEIRNSMIALIQRNKVITEGAGALACAALLSGKLDSHIQNRKTVSIISGGNIDLSRVSQITGLVD 328
               SCOP domains d2gn2a_ A: automated matches                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh..........hhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhh...........hhhhh....hhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhh..eeeeee.....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------DEHYDRATASE_SE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gn2 A   3 ITYDLPVAIEDILEAKKRLAGKIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFkIRGAFNKLSSLTEAEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVVLHGDNFNDTIAKVSEIVETEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVIVPIGGGGLIAGIAIAIKSINPTIKVIGVQAENVHGMAASYYTGEITTHRTTGTLADGCDVSRPGNLTYEIVRELVDDIVLVSEDEIRNSMIALIQRNKVITEGAGALACAALLSGKLDSHIQNRKTVSIISGGNIDLSRVSQITGLVD 328
                                    12        22        32        42        52     |  62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322      
                                                                                  58-LLP                                                                                                                                                                                                                                                                          

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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GN2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GN2)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (TDCB_SALTY | P11954)
molecular function
    GO:0003941    L-serine ammonia-lyase activity    Catalysis of the reaction: L-serine = pyruvate + NH3.
    GO:0004794    L-threonine ammonia-lyase activity    Catalysis of the reaction: L-threonine = 2-oxobutanoate + NH3.
    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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
    GO:0006565    L-serine catabolic process    The chemical reactions and pathways resulting in the breakdown of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0070689    L-threonine catabolic process to propionate    The chemical reactions and pathways resulting in the breakdown of L-threonine (the L-enantiomer of 2-amino-3-hydroxybutyric acid) to form the compound propionate.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    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.
    GO:0006567    threonine catabolic process    The chemical reactions and pathways resulting in the breakdown of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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        TDCB_SALTY | P119542gn0 2gn1

(-) Related Entries Specified in the PDB File

2gn0 DIMERIC STRUCTURE OF BIODEGRADATIVE THREONINE DEAMINASE (TDCB)AT 1.7A RESOLUTION IN TRICLINIC FORM WITH TWO DIMERS OF TDCB IN THE ASYMMETRIC UNIT
2gn1 DIMERIC STRUCTURE OF BIODEGRADATIVE THREONINE DEAMINASE (TDCB) AT 2.2A RESOLUTION IN TRICLINIC FORM WITH ONE DIMER OF TDCB IN THE ASYMMETRIC UNIT