Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  THREONINE DEAMINASE (BIOSYNTHETIC) FROM E. COLI
 
Authors :  D. T. Gallagher, G. L. Gilliland, G. Xiao, E. Eisenstein
Date :  27 Mar 98  (Deposition) - 14 Oct 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Allostery, Cooperative, Tetramer, Regulation, Pyridoxal Phosphate, Isoleucine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. T. Gallagher, G. L. Gilliland, G. Xiao, J. Zondlo, K. E. Fisher, D. Chinchilla, E. Eisenstein
Structure And Control Of Pyridoxal Phosphate Dependent Allosteric Threonine Deaminase.
Structure V. 6 465 1998
PubMed-ID: 9562556  |  Reference-DOI: 10.1016/S0969-2126(98)00048-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BIOSYNTHETIC THREONINE DEAMINASE
    Cellular LocationCYTOPLASM
    ChainsA
    EC Number4.2.1.16
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsSCHIFF BASE LINKAGE BETWEEN LYS 62 AND PLP
    SynonymTHREONINE DEHYDRATASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:61 , LYS A:62 , ASN A:89 , GLY A:188 , GLY A:189 , GLY A:190 , GLY A:191 , LEU A:192 , GLY A:241 , VAL A:242 , GLU A:286 , SER A:288 , SER A:315 , GLY A:316 , HOH A:614BINDING SITE FOR RESIDUE PLP A 962

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TDJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TDJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TDJ)

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDRATASE_SER_THRPS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.ILVA_ECOLI53-66  1A:53-66
2ACT_LIKEPS51672 ACT-like domain profile.ILVA_ECOLI339-411
434-504
  2A:339-411
A:434-504
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDRATASE_SER_THRPS00165 Serine/threonine dehydratases pyridoxal-phosphate attachment site.ILVA_ECOLI53-66  2A:53-66
2ACT_LIKEPS51672 ACT-like domain profile.ILVA_ECOLI339-411
434-504
  4A:339-411
A:434-504

(-) Exons   (0, 0)

(no "Exon" information available for 1TDJ)

(-) 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:494
 aligned with ILVA_ECOLI | P04968 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:510
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514
           ILVA_ECOLI     5 QPLSGAPEGAEYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHLDRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFELGDHEPDFETRLNELGYDCHDETNNPAFRFFLAG 514
               SCOP domains d1tdja1 A:5-335 Threonine deaminase                                                                                                                                                                                                                                                                                                        d1tdja2 A:336-423 Allosteric threonine deaminase C-terminal domain                      d1tdja3 A:424-514 Allosteric threonine deaminase C-termin                al domain          SCOP domains
               CATH domains 1tdjA01 A:5-64,A:157-319                                    1tdjA02 A:65-156  [code=3.40.50.1100, no name defined]                                      1tdjA01 A:5-64,A:157-319  [code=3.40.50.1100, no name defined]                                                                                                     ------------------1tdjA03 A:338-514 Biosynthetic Threonine Deaminase; Domain 3                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhh..hhh......eee.hhhhhh...eeeee.hhh.......hhhhhhhhh...........eeee....hhhhhhhhhh....eeee......hhhhhhhhhh..eee.....hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhh....eeeeeee....hhhhhhhh.......................hhhhhh.....eeeee.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhh....eeeeeee........hhhhhhh...eeeeee.........eeeeeee...hhhhhhhhhhhhh....eee.....hhhhh.hhh............eeeeee......hhhhhhhhh.......eee..........eeeee.----------------.eeee....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------DEHYDRATASE_SE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT_LIKE  PDB: A:339-411 UniProt: 339-411                                ----------------------ACT_LIKE  PDB: A:434-504 UniProt: 434-504                              ---------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tdj A   5 QPLSGAPEGAEYLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKREDRQPVHSFKLRGAYAMMAGLTEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATADIKVDAVRGFGGEVLLHGANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELLQQDAHLDRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPRVGLFAEGVAVKRIGDETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALAGMKKYIALHNIRGERLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKGSFLKFCQLLGGRSVTEFNYRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLSDDEMAKLHVRYMVGGRPSHPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGTDYGRVLAAFE----------------YDCHDETNNPAFRFFLAG 514
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474     |   -         -  |    504       514
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     480              497                 

   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, 3)

Asymmetric Unit

(-) CATH Domains  (2, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1TDJ)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (ILVA_ECOLI | P04968)
molecular function
    GO:0004794    L-threonine ammonia-lyase activity    Catalysis of the reaction: L-threonine = 2-oxobutanoate + NH3.
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    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: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:0009082    branched-chain amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    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:0009097    isoleucine biosynthetic process    The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid.
    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:0006566    threonine metabolic process    The chemical reactions and pathways involving 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    PLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1tdj)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1tdj
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ILVA_ECOLI | P04968
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.2.1.16
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  ILVA_ECOLI | P04968
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1TDJ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1TDJ)