Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
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 :  THYMIDYLATE SYNTHASE E60D MUTANT BINARY COMPLEX WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)
 
Authors :  D. L. Birdsall, J. Finer-Moore, R. M. Stroud
Date :  18 Sep 96  (Deposition) - 12 Mar 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Methyltransferase, Nucleotide Synthase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. L. Birdsall, W. Huang, D. V. Santi, R. M. Stroud, J. Finer-Moore
The Separate Effects Of E60Q In Lactobacillus Casei Thymidylate Synthase Delineate Between Mechanisms For Formation Of Intermediates In Catalysis.
Protein Eng. V. 11 171 1998
PubMed-ID: 9613841  |  Reference-DOI: 10.1093/PROTEIN/11.3.171
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    Chains: A
    EC Number: 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: THYMIDYLATE SYNTHASE
    Expression System Plasmid: PSCTS13
    Expression System Strain: X(CHI)2913 THY-
    Expression System Taxid: 562
    Gene: THYMIDYLATE SYNTHASE
    Mutation: YES
    Organism Scientific: LACTOBACILLUS CASEI
    Organism Taxid: 1582
    Synonym: TS, LCTS

 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
1UMP1Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:23 , ARG A:178 , ARG A:179 , LEU A:195 , HIS A:199 , GLN A:217 , ARG A:218 , SER A:219 , ALA A:220 , ASP A:221 , GLY A:225 , ASN A:229 , HIS A:259 , TYR A:261 , HOH A:334BINDING SITE FOR RESIDUE UMP A 317

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_SYNTHASEPS00091 Thymidylate synthase active site.TYSY_LACCA178-206  1A:178-206
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_SYNTHASEPS00091 Thymidylate synthase active site.TYSY_LACCA178-206  2A:178-206

(-) Exons   (0, 0)

(no "Exon" information available for 1VZA)

(-) 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:316
 aligned with TYSY_LACCA | P00469 from UniProtKB/Swiss-Prot  Length:316

    Alignment length:316
                                    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       270       280       290       300       310      
           TYSY_LACCA     1 MLEQPYLDLAKKVLDEGHFKPDRTHTGTYSIFGHQMRFDLSKGFPLLTTKKVPFGLIKSELLWFLHGDTNIRFLLQHRNHIWDEWAFEKWVKSDEYHGPDMTDFGHRSQKDPEFAAVYHEEMAKFDDRVLHDDAFAAKYGDLGLVYGSQWRAWHTSKGDTIDQLGDVIEQIKTHPYSRRLIVSAWNPEDVPTMALPPCHTLYQFYVNDGKLSLQLYQRSADIFLGVPFNIASYALLTHLVAHECGLEVGEFIHTFGDAHLYVNHLDQIKEQLSRTPRPAPTLQLNPDKHDIFDFDMKDIKLLNYDPYPAIKAPVAV 316
               SCOP domains d1vzaa_ A: Thymidylate synthase                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1vzaA00 A:1-316 Thymidylate Synthase, chain A                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains --Thymidylat_synt-1vzaA01 A:3-316                                                                                                                                                                                                                                                                                            Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh.eee.......eeeee.eeeeeehhh...........hhhhhhhhhhhhh....hhhhhhh...hhhhhhhhhh......................hhh..hhhhhhhhhhhh...hhhhhhh......hhhhhh...........hhhhhhhhhhh......eeee......hhh......eeeeeeeee..eeeeeeee.eee....hhhhhhhhhhhhhhhhhhh.....eeeeee.eeeeehhhhhhhhhhhh.......eeee......hhh.....eeee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vza A   1 MLEQPYLDLAKKVLDEGHFKPDRTHTGTYSIFGHQMRFDLSKGFPLLTTKKVPFGLIKSDLLWFLHGDTNIRFLLQHRNHIWDEWAFEKWVKSDEYHGPDMTDFGHRSQKAPEFAAVYHEEMAKFDDRVLHDDAFAAKYGDLGLVYGSQWRAWHTSKGDTIDQLGDVIEQIKTHPYSRRLIVSAWNPEDVPTMALPPCHTLYQFYVNDGKLSLQLYQRSADIFLGVPFNIASYALLTHLVAHECGLEVGEFIHTFGDAHLYVNHLDQIKEQLSRTPRPAPTLQLNPDKHDIFDFDMKDIKLLNYDPYPAIKAPVAV 316
                                    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       270       280       290       300       310
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Thymidylat_synt] (68)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (TYSY_LACCA | P00469)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0004799    thymidylate synthase activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dUMP = 7,8-dihydrofolate + thymidylate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006231    dTMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate).
    GO:0006235    dTTP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
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
    UMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1vza)
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1vza
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TYSY_LACCA | P00469
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.45
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  TYSY_LACCA | P00469
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TYSY_LACCA | P00469: 1bo7 1bo8 1bp0 1bp6 1bpj 1jmf 1jmg 1jmh 1jmi 1lca 1lcb 1lce 1nja 1njb 1njc 1njd 1nje 1tda 1tdb 1tdc 1thy 1tsl 1tsm 1tsv 1tsw 1tsx 1tsy 1tsz 1tvu 1tvv 1tvw 1vzb 1vzc 1vzd 1vze 2g86 2g89 2g8a 2g8d 2tdd 2tdm 3bnz 3byx 3bz0 3c06 3c0a 3ijz 3ik0 3ik1 4tms

(-) Related Entries Specified in the PDB File

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