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
(-)Biological Unit 1
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  E.COLI GDP-MANNOSE 4,6-DEHYDRATASE
 
Authors :  J. R. Somoza, S. Menon, W. S. Somers, F. X. Sullivan
Date :  02 Nov 99  (Deposition) - 24 Nov 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Dehydratase, Nadp, Gdp-Mannose, Gdp-Fucose, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Somoza, S. Menon, H. Schmidt, D. Joseph-Mccarthy, A. Dessen, M. L. Stahl, W. S. Somers, F. X. Sullivan
Structural And Kinetic Analysis Of Escherichia Coli Gdp-Mannose 4, 6 Dehydratase Provides Insights Into The Enzyme'S Catalytic Mechanism And Regulation By Gdp-Fucose.
Structure Fold. Des. V. 8 123 2000
PubMed-ID: 10673432  |  Reference-DOI: 10.1016/S0969-2126(00)00088-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GDP-MANNOSE 4,6-DEHYDRATASE
    Chains: A
    EC Number: 4.2.1.47
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7GMD
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1DB3)

(-) Sites  (0, 0)

(no "Site" information available for 1DB3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1DB3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile A:142 -Pro A:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DB3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1DB3)

(-) Exons   (0, 0)

(no "Exon" information available for 1DB3)

(-) 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:335
 aligned with GM4D_ECOLI | P0AC88 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:357
                                    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       271       281       291       301       311       321       331       341       351       
           GM4D_ECOLI     2 SKVALITGVTGQDGSYLAEFLLEKGYEVHGIKRRASSFNTERVDHIYQDPHTCNPKFHLHYGDLSDTSNLTRILREVQPDEVYNLGAMSHVAVSFESPEYTADVDAMGTLRLLEAIRFLGLEKKTRFYQASTSELYGLVQEIPQKETTPFYPRSPYAVAKLYAYWITVNYRESYGMYACNGILFNHESPRRGETFVTRKITRAIANIAQGLESCLYLGNMDSLRDWGHAKDYVKMQWMMLQQEQPEDFVIATGVQYSVRQFVEMAAAQLGIKLRFEGTGVEEKGIVVSVTGHDAPGVKPGDVIIAVDPRYFRPAEVETLLGDPTKAHEKLGWKPEITLREMVSEMVANDLEAAKKHS 358
               SCOP domains d1db3a_ A: GDP-mannose 4,6-dehydr                     atase                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1db3A01 A:1-191,A:227-254,A:315-3                     36 NAD(P)-binding Rossmann-like Domain                                                                                                   1db3A02                            1db3A01                     1db3A02 A:192-226,A:255-314,A:337-357                       1 db3A01              1db3A02               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeee..---------------------..eee......hhhhhhhhhhhhh..eeee............hhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhh................hhhhhhhhhhhhhhhhhhhhhh..eeeeee..ee.......hhhhhhhhhhhhhhh.....eee.....ee..eehhhhhhhhhhh........eee.....eehhhhhhhhhhh..eeeeee.hhhh.eeeeeee............eeeee.hhhh....-......hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1db3 A   1 SKVALITGVTGQDGSYLAEFLLEKGYEVHGIKR---------------------PKFHLHYGDLSDTSNLTRILREVQPDEVYNLGAMSHVAVSFESPEYTADVDAMGTLRLLEAIRFLGLEKKTRFYQASTSELYGLVQEIPQKETTPFYPRSPYAVAKLYAYWITVNYRESYGMYACNGILFNHESPRRGETFVTRKITRAIANIAQGLESCLYLGNMDSLRDWGHAKDYVKMQWMMLQQEQPEDFVIATGVQYSVRQFVEMAAAQLGIKLRFEGTGVEEKGIVVSVTGHDAPGVKPGDVIIAVDPRYFRPAE-ETLLGDPTKAHEKLGWKPEITLREMVSEMVANDLEAAKKHS 357
                                    10        20        30  |      -         -    |   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    | |320       330       340       350       
                                                           33                    55                                                                                                                                                                                                                                                                 315 |                                        
                                                                                                                                                                                                                                                                                                                                                      317
   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) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DB3)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (GM4D_ECOLI | P0AC88)
molecular function
    GO:0008446    GDP-mannose 4,6-dehydratase activity    Catalysis of the reaction: GDP-alpha-D-mannose = GDP-4-dehydro-6-deoxy-alpha-D-mannose + H(2)O.
    GO:0070401    NADP+ binding    Interacting selectively and non-covalently with the oxidized form, NADP+, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
    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.
biological process
    GO:0042351    'de novo' GDP-L-fucose biosynthetic process    The chemical reactions and pathways resulting in the formation of GDP-L-fucose from GDP-D-mannose via GDP-4-dehydro-6-deoxy-D-mannose, requiring the functions of GDP-mannose 4,6-dehydratase (EC:4.2.1.47) and GDP-L-fucose synthase (EC:1.1.1.271).
    GO:0019673    GDP-mannose metabolic process    The chemical reactions and pathways involving GDP-mannose, a substance composed of mannose in glycosidic linkage with guanosine diphosphate.
    GO:0009242    colanic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of colanic acid, a capsular bacterial polysaccharide.

 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 1db3)
 
  Sites
(no "Sites" information available for 1db3)
 
  Cis Peptide Bonds
    Ile A:142 - Pro A:143   [ RasMol ]  
 
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 | Biol. Unit 1 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
  1db3
    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
  GM4D_ECOLI | P0AC88
    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)
  4.2.1.47
    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
  GM4D_ECOLI | P0AC88
    Protein Disorder Prediction: DisEMBL | 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 1DB3)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1DB3)