Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
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 :  CRYSTAL STRUCTURE OF THE HIS281TYR MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
 
Authors :  H. R. Brodkin, M. J. Mcleish
Date :  20 Apr 13  (Deposition) - 08 May 13  (Release) - 08 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Thiamine Diphosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. R. Brodkin, F. H. Andrews, A. C. Milne, G. A. Petsko, D. Ringe, M. J. Mcleish
Crystal Structure Of The His281Tyr Mutant Of Benzoylformate Decarboxylase From Pseudomonas Putida
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BENZOYLFORMATE DECARBOXYLASE
    Chains: A
    EC Number: 4.1.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MDLC
    Mutation: YES
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
    Synonym: BFD, BFDC

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2MG3Ligand/IonMAGNESIUM ION
3TPP1Ligand/IonTHIAMINE DIPHOSPHATE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MG-1Ligand/IonMAGNESIUM ION
3TPP4Ligand/IonTHIAMINE DIPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:23 , PRO A:24 , GLY A:25 , GLU A:47 , HIS A:70 , ASN A:77 , GLU A:375 , THR A:377 , SER A:378 , GLY A:401 , LEU A:403 , GLY A:427 , ASP A:428 , GLY A:429 , SER A:430 , TYR A:433 , ASN A:455 , THR A:457 , TYR A:458 , GLY A:459 , ALA A:460 , LEU A:461 , CA A:602 , HOH A:746BINDING SITE FOR RESIDUE TPP A 601
2AC2SOFTWAREASP A:428 , ASN A:455 , THR A:457 , TPP A:601 , HOH A:739BINDING SITE FOR RESIDUE CA A 602
3AC3SOFTWAREASN A:117 , LEU A:118 , ARG A:120BINDING SITE FOR RESIDUE MG A 603
4AC4SOFTWAREARG A:184 , ASP A:187 , HOH A:921BINDING SITE FOR RESIDUE MG A 604
5AC5SOFTWAREASP A:347 , ALA A:416 , HOH A:824 , HOH A:847 , HOH A:881 , HOH A:989 , HOH A:1022BINDING SITE FOR RESIDUE MG A 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K9K)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Arg A:120 -Pro A:121
2Ala A:149 -Pro A:150
3Val A:277 -Phe A:278

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K9K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K9K)

(-) Exons   (0, 0)

(no "Exon" information available for 4K9K)

(-) 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:524
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4k9ka1 A:2-181 automated matches                                                                                                                                                   d4k9ka2 A:182-341 Benzoylformate decarboxylase                                                                                                                  d4k9ka3 A:342-525 automated matches                                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh........hhhhh......eee...hhhhhhhhhhhhhhhhhh.....eeeeee.hhh....hhhhhhhh..........hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh..eee...............eeee...hhhhhhhhhh...eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeeehhhhhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.............hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k9k A   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYYQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVS 525
                                    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       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521
   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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K9K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K9K)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TPP  [ 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 ]
 
  Cis Peptide Bonds
    Ala A:149 - Pro A:150   [ RasMol ]  
    Arg A:120 - Pro A:121   [ RasMol ]  
    Val A:277 - Phe A:278   [ 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 | 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
  4k9k
    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
  MDLC_PSEPU | P20906
    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)
  4.1.1.7
    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
  MDLC_PSEPU | P20906
    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
        MDLC_PSEPU | P20906: 1bfd 1mcz 1pi3 1po7 1q6z 1yno 2fn3 2fwn 2v3w 3f6b 3f6e 3fsj 3fzn 4gg1 4gm0 4gm1 4gm4 4gp9 4gpe 4jd5 4ju8 4ju9 4jua 4jub 4juc 4jud 4juf 4k9l 4k9m 4k9n 4k9o 4k9p 4mpj 4mpp 4mpr 4mq5 4mzx 4qel 5dei 5dgd 5dgt

(-) Related Entries Specified in the PDB File

4k9l THE HIS281THR MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
4k9m THE HIS281ASN MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
4k9n THE ALA460ILE MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
4k9o THE PHE397ALA MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
4k9p THE HIS281TYR/ALA460ILE DOUBLE MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA