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

(-) Description

Title :  CRYSTAL STRUCTURE OF P28L/Y173F TRYPTOPHAN SYNTHASE ALPHA-SUBUNITS FROM ESCHERICHIA COLI
 
Authors :  S. B. Jang
Date :  01 Sep 04  (Deposition) - 02 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Tryptophan Synthase, A-Subunits, E. Coli, P28L/Y173F Double Mutants, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. S. Jeong, J. K. Jeong, W. K. Lim, S. B. Jang
Structures Of Wild-Type And P28L/Y173F Tryptophan Synthase Alpha-Subunits From Escherichia Coli
Biochem. Biophys. Res. Commun. V. 323 1257 2004
PubMed-ID: 15451433  |  Reference-DOI: 10.1016/J.BBRC.2004.08.222
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPTOPHAN SYNTHASE ALPHA CHAIN
    ChainsA, B
    EC Number4.2.1.20
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTACTRPAMK-M13
    Expression System StrainRB797
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymTRYPTOPHAN SYNTHASE A-SUBUNITS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1XCF)

(-) Sites  (0, 0)

(no "Site" information available for 1XCF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRP_SYNTHASE_ALPHAPS00167 Tryptophan synthase alpha chain signature.TRPA_ECOLI48-61
 
  2A:48-54
B:48-54
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRP_SYNTHASE_ALPHAPS00167 Tryptophan synthase alpha chain signature.TRPA_ECOLI48-61
 
  4A:48-54
B:48-54

(-) Exons   (0, 0)

(no "Exon" information available for 1XCF)

(-) 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:238
 aligned with TRPA_ECOLI | P0A877 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:267
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       
           TRPA_ECOLI     1 MERYESLFAQLKERKEGAFVPFVTLGDPGIEQSLKIIDTLIEAGADALELGIPFSDPLADGPTIQNATLRAFAAGVTPAQCFEMLALIRQKHPTIPIGLLMYANLVFNKGIDEFYAQCEKVGVDSVLVADVPVEESAPFRQAALRHNVAPIFICPPNADDDLLRQIASYGRGYTYLLSRAGVTGAENRAALPLNHLVAKLKEYNAAPPLQGFGISAPDQVKAAIDAGAAGAISGSAIVKIIEQHINEPEKMLAALKVFVQPMKAATR 267
               SCOP domains d1xcfa_ A: Trp synthase alpha-subunit                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1xcfA00 A:1-267 Aldolase class I                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhh...eeee...---------------------.hhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh..ee..ee....hhhhhhhhhhhh...eee....--------...hhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeee.hhhhhhhhh...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------TRP_SYNTHASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xcf A   1 MERYESLFAQLKERKEGAFVPFVTLGDLGIEQSLKIIDTLIEAGADALELGIPF---------------------VTPAQCFEMLAIIREKHPTIPIGLLMYANLVFNKGIDEFYARCEKVGVDSVLVADVPVEESAPFRQAALRHNVAPIFICPPNADDDLLRQIASYGRGFTYLLSRA--------AALPLNHLVAKLKEYNAAPPLQGFGISAPDQVKAAIDAGAAGAISGSAIVKIIEQHINEPEKMLAALKVFVQPMKAATR 267
                                    10        20        30        40        50   |     -         -     |  80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       
                                                                                54                    76                                                                                                     180      189                                                                              

Chain B from PDB  Type:PROTEIN  Length:238
 aligned with TRPA_ECOLI | P0A877 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:267
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       
           TRPA_ECOLI     1 MERYESLFAQLKERKEGAFVPFVTLGDPGIEQSLKIIDTLIEAGADALELGIPFSDPLADGPTIQNATLRAFAAGVTPAQCFEMLALIRQKHPTIPIGLLMYANLVFNKGIDEFYAQCEKVGVDSVLVADVPVEESAPFRQAALRHNVAPIFICPPNADDDLLRQIASYGRGYTYLLSRAGVTGAENRAALPLNHLVAKLKEYNAAPPLQGFGISAPDQVKAAIDAGAAGAISGSAIVKIIEQHINEPEKMLAALKVFVQPMKAATR 267
               SCOP domains d1xcfb_ B: Trp synthase alpha-subunit                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1xcfB00 B:1-267 Aldolase class I                                                                                                                                                                                                                                            CATH domains
           Pfam domains (1) -------Trp_syntA-1xcfB01 B:8-267                                                                                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) -------Trp_syntA-1xcfB02 B:8-267                                                                                                                                                                                                                                            Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhh...eeee...---------------------.hhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh..ee..ee....hhhhhhhhhhhh...eee....--------...hhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeee.hhhhhhhhh...hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------TRP_SYNTHASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xcf B   1 MERYESLFAQLKERKEGAFVPFVTLGDLGIEQSLKIIDTLIEAGADALELGIPF---------------------VTPAQCFEMLAIIREKHPTIPIGLLMYANLVFNKGIDEFYARCEKVGVDSVLVADVPVEESAPFRQAALRHNVAPIFICPPNADDDLLRQIASYGRGFTYLLSRA--------AALPLNHLVAKLKEYNAAPPLQGFGISAPDQVKAAIDAGAAGAISGSAIVKIIEQHINEPEKMLAALKVFVQPMKAATR 267
                                    10        20        30        40        50   |     -         -     |  80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       
                                                                                54                    76                                                                                                     180      189                                                                              

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TRPA_ECOLI | P0A877)
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: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.
    GO:0004834    tryptophan synthase activity    Catalysis of the reaction: L-serine + (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H2O.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    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: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:0000162    tryptophan biosynthetic process    The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate.
    GO:0006568    tryptophan metabolic process    The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 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
(no "Ligands, Modified Residues, Ions" information available for 1xcf)
 
  Sites
(no "Sites" information available for 1xcf)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1xcf)
 
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
  1xcf
    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
  TRPA_ECOLI | P0A877
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.2.1.20
    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
  TRPA_ECOLI | P0A877
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TRPA_ECOLI | P0A8771v7y 1wq5 1xc4

(-) Related Entries Specified in the PDB File

1k8x ON THE ROLE OF ATHR183 IN THE ALLOSTERIC REGULATION AND CATALYTIC MECHANISM OF TRYPTOPHAN SYNTHASE
1xc4 CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE ALPHA- SUBUNITS FROM ESCHERICHIA COLI