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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SER26THR MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
 
Authors :  M. J. Mcleish, H. R. Brodkin
Date :  24 Mar 13  (Deposition) - 17 Apr 13  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  X
Biol. Unit 1:  X  (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 Ser26Thr Mutant Of Benzoylformate Decarboxylase From Pseudomonas Putida
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BENZOYLFORMATE DECARBOXYLASE
    Chains: X
    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 : X
Biological Unit 1 (4x): X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GOL5Ligand/IonGLYCEROL
3MG1Ligand/IonMAGNESIUM ION
4TZD1Ligand/Ion2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGENDIPHOSPHATE
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL20Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4TZD4Ligand/Ion2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGENDIPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN X:23 , PRO X:24 , GLY X:25 , GLU X:47 , HIS X:70 , ASN X:77 , GLU X:375 , THR X:377 , SER X:378 , GLY X:401 , LEU X:403 , GLY X:427 , ASP X:428 , GLY X:429 , SER X:430 , TYR X:433 , THR X:457 , TYR X:458 , GLY X:459 , ALA X:460 , CA X:603 , GOL X:605 , HOH X:714 , HOH X:779BINDING SITE FOR RESIDUE TZD X 601
2AC2SOFTWAREASN X:117 , LEU X:118 , ARG X:120BINDING SITE FOR RESIDUE MG X 602
3AC3SOFTWAREASP X:428 , ASN X:455 , THR X:457 , TZD X:601 , HOH X:704BINDING SITE FOR RESIDUE CA X 603
4AC4SOFTWAREARG X:13 , ASP X:38 , LYS X:504 , HOH X:866 , HOH X:944 , HOH X:1006BINDING SITE FOR RESIDUE GOL X 604
5AC5SOFTWAREHIS X:281 , THR X:377 , GLY X:401 , TZD X:601 , HOH X:927BINDING SITE FOR RESIDUE GOL X 605
6AC6SOFTWARETRP X:86 , GLU X:107 , ARG X:279 , ASP X:301 , LEU X:303 , GLU X:304 , ARG X:307 , HOH X:916BINDING SITE FOR RESIDUE GOL X 606
7AC7SOFTWAREALA X:196 , ARG X:294 , ASP X:312 , HOH X:979BINDING SITE FOR RESIDUE GOL X 607
8AC8SOFTWAREALA X:102 , GLY X:105 , GLU X:134 , HIS X:137 , ASP X:168 , TYR X:288 , HOH X:784 , HOH X:805 , HOH X:967BINDING SITE FOR RESIDUE GOL X 608

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JUD)

(-) 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 X from PDB  Type:PROTEIN  Length:525
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4judx1 X:2-181 automated matches                                                                                                                                                   d4judx2 X:182-341 Benzoylformate decarboxylase                                                                                                                  d4judx3 X:342-526 automated matches                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh........hhhhh.......ee...hhhhhhhhhhhhhhhhhh.....eeeeee........hhhhhhhh..........hhhhhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhh..eee...............eeee...hhhhhhhhh....eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeee...hhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jud X   2 ASVHGTTYELLRRQGIDTVFGNPGTNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSP 526
                                    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 4JUD)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala X:149 - Pro X:150   [ RasMol ]  
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    Val X:277 - Phe X:278   [ RasMol ]  
 
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  4.1.1.7
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 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 4juf 4k9k 4k9l 4k9m 4k9n 4k9o 4k9p 4mpj 4mpp 4mpr 4mq5 4mzx 4qel 5dei 5dgd 5dgt

(-) Related Entries Specified in the PDB File

4ju8 THE HIS70PHE MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
4ju9 THE HIS70LEU MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
4jua THE HIS70SER MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
4jub THE HIS70THR MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
4juc THE SER26MET MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
4juf THE HIS281ALA MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA