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
(-)Biological Unit 2
(-)Biological Unit 3
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPTOPHAN SYNTHASE ALPHA CHAIN HOMOLOG BX1: A MEMBER OF THE CHEMICAL PLANT DEFENSE SYSTEM
 
Authors :  V. Kulik, E. Hartmann, M. Weyand, M. Frey, A. Gierl, D. Niks, M. F. Dunn, I. Schlichting
Date :  05 Nov 03  (Deposition) - 28 Dec 04  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (4x)
Keywords :  Hydroxamic Acid, Diboa, Dimboa, Indole, Indole-Glycerol-Phosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Kulik, E. Hartmann, M. Weyand, M. Frey, A. Gierl, D. Niks, M. F. Dunn, I. Schlichting
On The Structural Basis Of The Catalytic Mechanism And The Regulation Of The Alpha Subunit Of Tryptophan Synthase From Salmonella Typhimurium And Bx1 From Maize, Two Evolutionarily Related Enzymes.
J. Mol. Biol. V. 352 608 2005
PubMed-ID: 16120446  |  Reference-DOI: 10.1016/J.JMB.2005.07.014
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRYPTOPHAN SYNTHASE ALPHA CHAIN, CHLOROPLAST
    ChainsA, B
    EC Number4.2.1.20
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificZEA MAYS
    Organism Taxid4577
    SynonymBX1, TRYPTOPHAN SYNTHASE ALPHA HOMOLOG

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (4x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MLA2Ligand/IonMALONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MLA1Ligand/IonMALONIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MLA1Ligand/IonMALONIC ACID
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1MLA8Ligand/IonMALONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:129 , ARG B:158 , HOH B:402 , HOH B:413BINDING SITE FOR RESIDUE MLA B 301
2AC2SOFTWAREALA A:132 , ARG A:158 , ALA A:165 , HOH A:395 , HOH A:415 , ARG B:158BINDING SITE FOR RESIDUE MLA A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RD5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:28 -Pro A:29
2Asp B:28 -Pro B:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RD5)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRP_SYNTHASE_ALPHAPS00167 Tryptophan synthase alpha chain signature.TRPA_MAIZE134-147
 
  2A:49-62
B:49-62
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRP_SYNTHASE_ALPHAPS00167 Tryptophan synthase alpha chain signature.TRPA_MAIZE134-147
 
  1A:49-62
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRP_SYNTHASE_ALPHAPS00167 Tryptophan synthase alpha chain signature.TRPA_MAIZE134-147
 
  1-
B:49-62
Biological Unit 3 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRP_SYNTHASE_ALPHAPS00167 Tryptophan synthase alpha chain signature.TRPA_MAIZE134-147
 
  8A:49-62
B:49-62

(-) Exons   (0, 0)

(no "Exon" information available for 1RD5)

(-) 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:261
 aligned with TRPA_MAIZE | P42390 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:261
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346 
           TRPA_MAIZE    87 SRPVSDTMAALMAKGKTAFIPYITAGDPDLATTAEALRLLDGCGADVIELGVPCSDPYIDGPIIQASVARALASGTTMDAVLEMLREVTPELSCPVVLLSYYKPIMSRSLAEMKEAGVHGLIVPDLPYVAAHSLWSEAKNNNLELVLLTTPAIPEDRMKEITKASEGFVYLVSVNGVTGPRANVNPRVESLIQEVKKVTNKPVAVGFGISKPEHVKQIAQWGADGVIIGSAMVRQLGEAASPKQGLRRLEEYARGMKNALP 347
               SCOP domains d1rd5a_ A: Trp synthase alpha-subunit                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1rd5A00 A:2-262 Aldolase class I                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeee..hhhhhh..hhhhhhh...eee.......hhhhhhhhhhhh..ee.eee....hhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------TRP_SYNTHASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rd5 A   2 SRPVSDTMAALMAKGKTAFIPYITAGDPDLATTAEALRLLDGCGADVIELGVPCSDPYIDGPIIQASVARALASGTTMDAVLEMLREVTPELSCPVVLLSYYKPIMFRSLAKMKEAGVHGLIVPDLPYVAAHSLWSEAKNNNLELVLLTTPAIPEDRMKEITKASEGFVYLVSVNGVTGPRANVNPRVESLIQEVKKVTNKPVAVGFGISKPEHVKQIAQWGADGVIIGSAMVRQLGEAASPKQGLRRLEEYARGMKNALG 262
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261 

Chain B from PDB  Type:PROTEIN  Length:248
 aligned with TRPA_MAIZE | P42390 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:261
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346 
           TRPA_MAIZE    87 SRPVSDTMAALMAKGKTAFIPYITAGDPDLATTAEALRLLDGCGADVIELGVPCSDPYIDGPIIQASVARALASGTTMDAVLEMLREVTPELSCPVVLLSYYKPIMSRSLAEMKEAGVHGLIVPDLPYVAAHSLWSEAKNNNLELVLLTTPAIPEDRMKEITKASEGFVYLVSVNGVTGPRANVNPRVESLIQEVKKVTNKPVAVGFGISKPEHVKQIAQWGADGVIIGSAMVRQLGEAASPKQGLRRLEEYARGMKNALP 347
               SCOP domains d1rd5b_ B: Trp synthase alpha-subunit                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1rd5B00 B:2-262 Aldolase class I                                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) -------Trp_syntA-1rd5B01 B:9-261                                                                                                                                                                                                                                    - Pfam domains (1)
           Pfam domains (2) -------Trp_syntA-1rd5B02 B:9-261                                                                                                                                                                                                                                    - Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhh....eeee......--.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeee..hhhhh..hhhhhhhh.eeeee....hhhhhhhhhhhhhhh..ee.eee....hhhhhhhhhhhh...eee...-----------.hhhhhhhhhhhhh...eee.....hhhhhhhhhhh...eeeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------TRP_SYNTHASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rd5 B   2 SRPVSDTMAALMAKGKTAFIPYITAGDPDLATTAEALRLLDGCGADVIELGVPCSDP--DGPIIQASVARALASGTTMDAVLEMLREVTPELSCPVVLLSYYKPIMFRSLAKMKEAGVHGLIVPDLPYVAAHSLWSEAKNNNLELVLLTTPAIPEDRMKEITKASEGFVYLVSV-----------PRVESLIQEVKKVTNKPVAVGFGISKPEHVKQIAQWGADGVIIGSAMVRQLGEAASPKQGLRRLEEYARGMKNALG 262
                                    11        21        31        41        51      | 61        71        81        91       101       111       121       131       141       151       161       171   |     -     | 191       201       211       221       231       241       251       261 
                                                                                   58 61                                                                                                               175         187                                                                           

   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  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TRPA_MAIZE | P42390)
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:0033984    indole-3-glycerol-phosphate lyase activity    Catalysis of the reaction: (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = indole + D-glyceraldehyde 3-phosphate.
    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: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:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

 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
    MLA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:28 - Pro A:29   [ RasMol ]  
    Asp B:28 - Pro B:29   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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
  1rd5
    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_MAIZE | P42390
    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_MAIZE | P42390
    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_MAIZE | P423901tjr

(-) Related Entries Specified in the PDB File

1bks TRYPTOPHAN SYNTHASE (E.C. 4.2.1.20) FROM SALMONELLA TYPHIMURIUM
1kfk CRYSTAL STRUCTURE OF TRYPTOPHAN SYNTHASE FROM SALMONELLA TYPHIMURIUM