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 BIOH AT 1.7 A
 
Authors :  R. Sanishvili, A. Savchenko, T. Skarina, A. Edwards, A. Joachimiak, A. Midwest Center For Structural Genomics (Mcsg)
Date :  26 Jun 02  (Deposition) - 21 Jan 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Betta-Alpha Sandwich, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Sanishvili, A. F. Yakunin, R. A. Laskowski, T. Skarina, E. Evdokimova, A. Doherty-Kirby, G. A. Lajoie, J. M. Thornton, C. H. Arrowsmith, A. Savchenko, A. Joachimiak, A. M. Edwards
Integrating Structure, Bioinformatics, And Enzymology To Discover Function: Bioh, A New Carboxylesterase From Escherichia Coli.
J. Biol. Chem. V. 278 26039 2003
PubMed-ID: 12732651  |  Reference-DOI: 10.1074/JBC.M303867200

(-) Compounds

Molecule 1 - BIOH PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BIOH
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
13OH1Ligand/Ion3-HYDROXY-PROPANOIC ACID
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:21 , TRP A:22 , LEU A:24 , TRP A:81 , SER A:82 , LEU A:83 , PHE A:111 , PHE A:143 , GLN A:147 , LEU A:183 , HIS A:235BINDING SITE FOR RESIDUE 3OH A 300
2AC2SOFTWAREGLU A:152 , LEU A:206 , LYS A:232BINDING SITE FOR RESIDUE EDO A 301
3AC3SOFTWAREILE A:229 , HIS A:241 , PRO A:242 , ALA A:243 , GLU A:244 , HOH A:360 , HOH A:424 , HOH A:510BINDING SITE FOR RESIDUE EDO A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M33)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M33)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M33)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M33)

(-) Exons   (0, 0)

(no "Exon" information available for 1M33)

(-) 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:256
 aligned with BIOH_ECOLI | P13001 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:256
                                                                                                                                                                                                                                                                                       256  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252   |  
           BIOH_ECOLI     3 NIWWQTKGQGNVHLVLLHGWGLNAEVWRCIDEELSSHFTLHLVDLPGFGRSRGFGALSLADMAEAVLQQAPDKAIWLGWSLGGLVASQIALTHPERVQALVTVASSPCFSARDEWPGIKPDVLAGFQQQLSDDFQRTVERFLALQTMGTETARQDARALKKTVLALPMPEVDVLNGGLEILKTVDLRQPLQNVSMPFLRLYGYLDGLVPRKVVPMLDKLWPHSESYIFAKAAHAPFISHPAEFCHLLVALKQRV--   -
               SCOP domains d1m33a_ A: Biotin biosynthesis protein BioH                                                                                                                                                                                                                      SCOP domains
               CATH domains 1m33A00 A:3-258  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                            CATH domains
               Pfam domains -------------------------------------Abhydrolase_1-1m33A01 A:40-251                                                                                                                                                                                      ------- Pfam domains
         Sec.struct. author ...eeee.....eeeee.....hhhhhhhhhhhhhh..eeeee..............hhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhh...eeeeeee...............hhhhhhhhhhhhhhhhhhhhhh.hhhhh....hhhhhhhhh.hhh......hhhhhhhhhhhhhhh...hhhhhh...eeeeee........hhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m33 A   3 NIWWQTKGQGNVHLVLLHGWGLNAEVWRCIDEELSSHFTLHLVDLPGFGRSRGFGALSLADmAEAVLQQAPDKAIWLGWSLGGLVASQIALTHPERVRALVTVASSPCFSARDEWPGIKPDVLAGFQQQLSDDQQRTVERFLALQTmGTETARQDARALKKTVLALPmPEVDVLNGGLEILKTVDLRQPLQNVSmPFLRLYGYLDGLVPRKVVPmLDKLWPHSESYIFAKAAHAPFISHPAEFCHLLVALKQRVGS 258
                                    12        22        32        42        52        62 |      72        82        92       102       112       122       132       142      |152       162       172       182       192    |  202       212    |  222       232       242       252      
                                                                                        64-MSE                                                                              149-MSE              170-MSE                    197-MSE             217-MSE
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: AB_hydrolase (347)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BIOH_ECOLI | P13001)
molecular function
    GO:0052689    carboxylic ester hydrolase activity    Catalysis of the hydrolysis of a carboxylic ester bond.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0090499    pimelyl-[acyl-carrier protein] methyl ester esterase activity    Catalysis of the reaction: pimelyl-[acyl-carrier protein] methyl ester + H2O = pimelyl-[acyl-carrier protein] + methanol.
biological process
    GO:0009102    biotin biosynthetic process    The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.
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/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
    3OH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1m33)
 

(-) 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
  1m33
    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
  BIOH_ECOLI | P13001
    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)
  (no 'Enzyme Classificator' available)
    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
  BIOH_ECOLI | P13001
    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 1M33)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1M33)