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

(-) Description

Title :  CRYSTAL STRUCTURE OF AMYLOSUCRASE DOUBLE MUTANT A289P-F290L FROM NEISSERIA POLYSACCHAREA
 
Authors :  F. Guerin, E. Champion, C. Moulis, S. Barbe, T. H. Tran, S. Morel, K. Desc P. Monsan, L. A. Mulard, M. Remaud-Simeon, I. Andre, L. Mourey, S. Tran
Date :  15 Jun 12  (Deposition) - 31 Oct 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta/Alpha-Barrel, Glycoside Hydrolase, Amylose Synthesis, Sucrose Isomerization, Glucosyltransferase, Carbohydrate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Champion, F. Guerin, C. Moulis, S. Barbe, T. H. Tran, S. Morel, K. Descroix, P. Monsan, L. Mourey, L. A. Mulard, S. Tranier, M. Remaud-Simeon, I. Andre
Applying Pairwise Combinations Of Amino Acid Mutations For Sorting Out Highly Efficient Glucosylation Tools For Chemo-Enzymatic Synthesis Of Bacterial Oligosaccharides.
J. Am. Chem. Soc. V. 134 18677 2012
PubMed-ID: 23072374  |  Reference-DOI: 10.1021/JA306845B

(-) Compounds

Molecule 1 - AMYLOSUCRASE
    Chains: A
    EC Number: 2.4.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX6P3
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: AMYLOSUCRASE (UNP RESIDUES 13-636)
    Gene: AMS
    Mutation: YES
    Organism Scientific: NEISSERIA POLYSACCHAREA
    Organism Taxid: 489

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric/Biological Unit (3, 20)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2GOL18Ligand/IonGLYCEROL
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:144 , TYR A:147 , HIS A:187 , PHE A:250 , ASP A:286 , GLU A:328 , ARG A:509 , GOL A:708 , GOL A:717 , HOH A:875BINDING SITE FOR RESIDUE TRS A 701
02AC2SOFTWAREASP A:403BINDING SITE FOR RESIDUE GOL A 702
03AC3SOFTWAREHIS A:332 , PHE A:399 , ASP A:401 , GLU A:402 , ARG A:415BINDING SITE FOR RESIDUE GOL A 703
04AC4SOFTWAREGLU A:328 , ILE A:330 , TYR A:349 , TYR A:388 , SER A:391 , HIS A:392 , ASP A:393 , GOL A:717 , HOH A:1000BINDING SITE FOR RESIDUE GOL A 704
05AC5SOFTWAREARG A:86 , GLU A:87 , PRO A:90 , ARG A:317 , PRO A:321 , PHE A:324 , GOL A:706 , HOH A:835 , HOH A:921 , HOH A:922BINDING SITE FOR RESIDUE GOL A 705
06AC6SOFTWAREPRO A:90 , ARG A:317 , PHE A:324 , GLN A:342 , GLN A:346 , HIS A:382 , GOL A:705BINDING SITE FOR RESIDUE GOL A 706
07AC7SOFTWAREASP A:91 , LEU A:94 , SER A:95 , ASP A:552 , GLY A:553 , HOH A:964BINDING SITE FOR RESIDUE GOL A 707
08AC8SOFTWARETYR A:104 , MET A:133 , ASP A:144 , GLY A:145 , TYR A:147 , HIS A:392 , ASP A:393 , ARG A:509 , ARG A:513 , TRS A:701 , HOH A:875 , HOH A:1004BINDING SITE FOR RESIDUE GOL A 708
09AC9SOFTWAREGLY A:396 , TRP A:397 , THR A:398 , ASP A:444 , CYS A:445 , ARG A:446BINDING SITE FOR RESIDUE GOL A 709
10BC1SOFTWAREARG A:226 , ILE A:228 , GLU A:328 , ALA A:329 , ILE A:330 , GOL A:717BINDING SITE FOR RESIDUE GOL A 710
11BC2SOFTWAREPHE A:229 , GLN A:232 , ASN A:251 , GLN A:437 , ASP A:506 , ASP A:507 , ARG A:509BINDING SITE FOR RESIDUE GOL A 711
12BC3SOFTWARETYR A:51 , ASN A:54 , SER A:260 , ASN A:562 , THR A:589 , THR A:592BINDING SITE FOR RESIDUE GOL A 712
13BC4SOFTWAREILE A:93 , LEU A:94 , SER A:95 , GLY A:480 , LEU A:481 , ARG A:545 , PHE A:551 , GLY A:553BINDING SITE FOR RESIDUE GOL A 713
14BC5SOFTWAREGLU A:55 , VAL A:366 , PHE A:559 , ASN A:560 , THR A:561 , ASN A:563 , LYS A:564 , ILE A:566 , HOH A:993 , HOH A:994 , HOH A:1012BINDING SITE FOR RESIDUE GOL A 714
15BC6SOFTWAREASN A:424 , PHE A:426 , ASP A:427 , GLY A:428 , SER A:429 , HOH A:1035BINDING SITE FOR RESIDUE GOL A 715
16BC7SOFTWAREASN A:207 , ASN A:258 , SER A:260 , HIS A:591 , GLN A:594BINDING SITE FOR RESIDUE GOL A 716
17BC8SOFTWAREPHE A:229 , GLU A:328 , ASP A:393 , ASP A:394 , PHE A:436 , ARG A:446 , TRS A:701 , GOL A:704 , GOL A:710BINDING SITE FOR RESIDUE GOL A 717
18BC9SOFTWARETRP A:194 , GLU A:271 , 1PE A:720BINDING SITE FOR RESIDUE GOL A 718
19CC1SOFTWAREASP A:202 , PRO A:203 , ASP A:526BINDING SITE FOR RESIDUE GOL A 719
20CC2SOFTWARELEU A:204 , PHE A:205 , PHE A:208 , TRP A:263 , ARG A:266 , ALA A:267 , GOL A:718 , HOH A:879 , HOH A:1013BINDING SITE FOR RESIDUE 1PE A 720

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FLR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FLR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FLR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FLR)

(-) Exons   (0, 0)

(no "Exon" information available for 4FLR)

(-) 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:628
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4flra1 A:1-554 automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         d4flra2 A:555-628 automated matches                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhh..eeee...ee.....hhhhh...eeeee.....hhhhhhhhhhhhhhh..eeeeee...eee..hhhhhhhhhhhhhhh....ee..hhhhhhhhh.............eee.....eee......eee....hhhhhhhhhhhhhhhhhh...eeee.hhhhh..........hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhh......eeehhhhhhhhhhhhhhh.hhhhhhhhhhh.......eeeee...........hhhhhhhh..hhhhhhhhhhhhhh..........eee.........eee.hhhhhhh......hhhhhhhhhhhhhhhh..eeeee.hhhhh...............hhhhhhh...hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh....ee.......eeeeee...eeeeee.....eee..........eeee.....eee....eee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4flr A   1 SPNSQYLKTRILDIYTPEQRAGIEKSEDWRQFSRRMDTHFPKLMNELDSVYGNNEALLPMLEMLLAQAWQSYSQRNSSLKDIDIARENNPDWILSNKQVGGVCYVDLFAGDLKGLKDKIPYFQELGLTYLHLMPLFKCPEGKSDGGYAVSSYRDVNPALGTIGDLREVIAALHEAGISAVVDFIFNHTSNEHEWAQRCAAGDPLFDNFYYIFPDRRMPDQYDRTLREIFPDQHPGGFSQLEDGRWVWTTFNSFQWDLNYSNPWVFRAMAGEMLFLANLGVDILRMDAVPLIWKQMGTSCENLPQAHALIRAFNAVMRIAAPAVFFKSEAIVHPDQVVQYIGQDECQIGYNPLQMALLWNTLATREVNLLHQALTYRHNLPEHTAWVNYVRSHDDIGWTFADEDAAYLGISGYDHRQFLNRFFVNRFDGSFARGVPFQYNPSTGDCRVSGTAAALVGLAQDDPHAVDRIKLLYSIALSTGGLPLIYLGDEVGTLNDDDWSQDSNKSDDSRWAHRPRYNEALYAQRNDPSTAAGQIYQDLRHMIAVRQSNPRFDGGRLVTFNTNNKHIIGYIRNNALLAFGNFSEYPQTVTAHTLQAMPFKAHDLIGGKTVSLNQDLTLQPYQVMWLEIA 628
                                    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       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FLR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FLR)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TRS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4flr)
 

(-) 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 | Asym./Biol. Unit - 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
  4flr
    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
  AMYS_NEIPO | Q9ZEU2
    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)
  2.4.1.4
    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
  AMYS_NEIPO | Q9ZEU2
    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
        AMYS_NEIPO | Q9ZEU2: 1g5a 1jg9 1jgi 1mvy 1mw0 1mw1 1mw2 1mw3 1s46 1zs2 3ueq 4flo 4flq 4fls 5n7j

(-) Related Entries Specified in the PDB File

1g5a CRYSTAL STRUCTURE OF THE WILD TYPE AMYLOSUCRASE FROM NEISSERIA POLYSACCHAREA
4flo CRYSTAL STRUCTURE OF AMYLOSUCRASE DOUBLE MUTANT A289P-F290C FROM NEISSERIA POLYSACCHAREA
4flq RYSTAL STRUCTURE OF AMYLOSUCRASE DOUBLE MUTANT A289P-F290I FROM NEISSERIA POLYSACCHAREA
4fls