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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE ALGINATE LYASE FROM CORYNEBACTERIUM SP.
 
Authors :  Y. Kakuta
Date :  11 Mar 03  (Deposition) - 27 Jul 04  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Jellyroll Beta-Sandwich, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Osawa, Y. Matsubara, T. Muramatsu, M. Kimura, Y. Kakuta
Crystal Structure Of The Alginate (Poly Alpha-L-Guluronate) Lyase From Corynebacterium Sp. At 1. 2 A Resolution
J. Mol. Biol. V. 345 1111 2005
PubMed-ID: 15644208  |  Reference-DOI: 10.1016/J.JMB.2004.10.081

(-) Compounds

Molecule 1 - POLYGULURONATE LYASE
    Chains: A
    EC Number: 4.2.2.11
    Organism Scientific: CORYNEBACTERIUM SP.
    Organism Taxid: 1720
    Synonym: ALGINATE LYASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1UAI)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:51
2A:200 -A:206

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Glu A:2 -Pro A:3
2Gln A:33 -Pro A:34
3Ala A:42 -Pro A:43
4Ser A:204 -Pro A:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UAI)

(-) Sequences/Alignments

Asymmetric/Biological 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:223
 aligned with Q9RB42_9CORY | Q9RB42 from UniProtKB/TrEMBL  Length:256

    Alignment length:223
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253   
         Q9RB42_9CORY    34 EPCDYPAQQLDLTDWKVTLPIGSSGKPSEIEQPALDTFATAPWFQVNAKCTGVQFRAAVNGVTTSGSGYPRSELREMTDGGEEKASWSATSGTHTMVFREAFNHLPEVKPHLVGAQIHDGDDDVTVFRLEGTSLYITKGDDTHHKLVTSDYKLNTVFEGKFVVSGGKIKVYYNGVLQTTISHTSSGNYFKAGAYTQANCSNSSPCSSSNYGQVSLYKLQVTHS 256
               SCOP domains d1uaia_ A: Polyguluronate lyase                                                                                                                                                                                                 SCOP domains
               CATH domains 1uaiA00 A:2-224  [code=2.60.120.200, no name defined]                                                                                                                                                                           CATH domains
               Pfam domains ---------Alginate_lyase2-1uaiA01 A:11-223                                                                                                                                                                                     - Pfam domains
         Sec.struct. author ....hhhhh.....eeeeeeeee..eeeee..hhhhhh.....eee......eeeeee............eeeeeeee....ee........eeeeeeeeeeee......eeeeeeee....eeeeeeee..eeeeee..eeeeeeee........eeeeeeee..eeeeee..eeeeeee......eeeeeeee..............eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uai A   2 EPCDYPAQQLDLTDWKVTLPIGSSGKPSEIEQPALDTFATAPWFQVNAKCTGVQFRAAVNGVTTSGSGYPRSELREMTDGGEEKASWSATSGTHTMVFREAFNHLPEVKPHLVGAQIHDGDDDVTVFRLEGTSLYITKGDDTHHKLVTSDYKLNTVFEGKFVVSGGKIKVYYNGVLQTTISHTSSGNYFKAGAYTQANCSNSSPCSSSNYGQVSLYKLQVTHS 224
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Alginate_lyase2] (7)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9RB42_9CORY | Q9RB42)
molecular function
    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:0047491    poly(alpha-L-guluronate) lyase activity    Catalysis of the reaction: polysaccharides containing a terminal alpha-L-guluronate group = oligosaccharides with 4-deoxy-alpha-L-erythro-hex-4-enuronosyl end. This reaction is the eliminative cleavage of polysaccharides containing a terminal a-L-guluronate group, to give oligopolysaccharides with 4-deoxy-a-L-erythro-hex-4-enuronosyl groups at their nonreducing ends.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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 1uai)
 
  Sites
(no "Sites" information available for 1uai)
 
  Cis Peptide Bonds
    Ala A:42 - Pro A:43   [ RasMol ]  
    Gln A:33 - Pro A:34   [ RasMol ]  
    Glu A:2 - Pro A:3   [ RasMol ]  
    Ser A:204 - Pro A:205   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  1uai
    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
  Q9RB42_9CORY | Q9RB42
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  4.2.2.11
    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
  Q9RB42_9CORY | Q9RB42
    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 1UAI)

(-) Related Entries Specified in the PDB File

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