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(-) Description

Title :  STRUCTURE OF BENZALDEHYDE LYASE A28S MUTANT WITH BENZOYLPHOSPHONATE
 
Authors :  G. S. Brandt, G. A. Petsko, D. Ringe, M. J. Mcleish
Date :  13 Jul 09  (Deposition) - 02 Mar 10  (Release) - 02 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Thiamine Adduct, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. S. Brandt, M. M. Kneen, G. A. Petsko, D. Ringe, M. J. Mcleish
Active-Site Engineering Of Benzaldehyde Lyase Shows That A Point Mutation Can Confer Both New Reactivity And Susceptibility To Mechanism-Based Inhibition.
J. Am. Chem. Soc. V. 132 438 2010
PubMed-ID: 20030408  |  Reference-DOI: 10.1021/JA907064W

(-) Compounds

Molecule 1 - BENZALDEHYDE LYASE
    Chains: A, B
    EC Number: 4.1.2.38
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BZNB
    Mutation: YES
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 294
    Strain: BIOVAR I

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2D7K2Ligand/Ion3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(S)-HYDROXY[(R)-HYDROXY(METHOXY)PHOSPHORYL]PHENYLMETHYL}-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2D7K4Ligand/Ion3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(S)-HYDROXY[(R)-HYDROXY(METHOXY)PHOSPHORYL]PHENYLMETHYL}-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:393 , ALA A:394 , LEU A:395 , THR A:396 , TYR A:397 , GLY A:419 , SER A:420 , MET A:421 , GLY A:447 , ASP A:448 , GLY A:449 , SER A:450 , TYR A:453 , ASN A:475 , SER A:477 , TRP A:478 , GLY A:479 , ALA A:480 , THR A:481 , CA A:572 , HOH A:574 , HIS B:26 , GLY B:27 , SER B:28 , GLU B:50 , THR B:73 , GLY B:76 , ASN B:80 , GLN B:113BINDING SITE FOR RESIDUE D7K A 571
2AC2SOFTWAREGLY A:447 , ASP A:448 , MET A:473 , ASN A:475 , D7K A:571BINDING SITE FOR RESIDUE CA A 572
3AC3SOFTWAREHIS A:26 , GLY A:27 , SER A:28 , GLU A:50 , THR A:73 , GLY A:76 , ASN A:80 , GLN A:113 , GLY B:393 , ALA B:394 , LEU B:395 , THR B:396 , TYR B:397 , GLY B:419 , SER B:420 , MET B:421 , GLY B:447 , ASP B:448 , GLY B:449 , SER B:450 , TYR B:453 , ASN B:475 , SER B:477 , TRP B:478 , GLY B:479 , ALA B:480 , THR B:481 , CA B:572 , HOH B:573BINDING SITE FOR RESIDUE D7K B 571
4AC4SOFTWAREGLY B:447 , ASP B:448 , MET B:473 , ASN B:475 , D7K B:571BINDING SITE FOR RESIDUE CA B 572

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IAE)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:152 -Pro A:153
2Ala B:152 -Pro B:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IAE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IAE)

(-) Exons   (0, 0)

(no "Exon" information available for 3IAE)

(-) 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:554
 aligned with Q9F4L3_PSEFL | Q9F4L3 from UniProtKB/TrEMBL  Length:563

    Alignment length:554
                                    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       531       541       551    
         Q9F4L3_PSEFL     2 AMITGGELVVRTLIKAGVEHLFGLHGAHIDTIFQACLDHDVPIIDTRHEAAAGHAAEGYARAGAKLGVALVTAGGGFTNAVTPIANAWLDRTPVLFLTGSGALRDDETNTLQAGIDQVAMAAPITKWAHRVMATEHIPRLVMQAIRAALSAPRGPVLLDLPWDILMNQIDEDSVIIPDLVLSAHGARPDPADLDQALALLRKAERPVIVLGSEASRTARKTALSAFVAATGVPVFADYEGLSMLSGLPDAMRGGLVQNLYSFAKADAAPDLVLMLGARFGLNTGHGSGQLIPHSAQVIQVDPDACELGRLQGIALGIVADVGGTIEALAQATAQDAAWPDRGDWCAKVTDLAQERYASIAAKSSSEHALHPFHASQVIAKHVDAGVTVVADGALTYLWLSEVMSRVKPGGFLCHGYLGSMGVGFGTALGAQVADLEAGRRTILVTGDGSVGYSIGEFDTLVRKQLPLIVIIMNNQSWGATLHFQQLAVGPNRVTGTRLENGSYHGVAAAFGADGYHVDSVESFSAALAQALAHNRPACINVAVALDPIPPEELI 555
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3iaeA01 A:2-183  [code=3.40.50.970, no name defined]                                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhh...eee..hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee...............hhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhh.....eeeeeehhhhhheee..................hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eeehhhhhhhhh..hhh.eeee.hhhhhhh.......eeeee....................eeeee..hhhhh.......eee..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh.....eee.........hhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh.............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee......hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iae A   2 AMITGGELVVRTLIKAGVEHLFGLHGSHIDTIFQACLDHDVPIIDTRHEAAAGHAAEGYARAGAKLGVALVTAGGGFTNAVTPIANAWLDRTPVLFLTGSGALRDDETNTLQAGIDQVAMAAPITKWAHRVMATEHIPRLVMQAIRAALSAPRGPVLLDLPWDILMNQIDEDSVIIPDLVLSAHGARPDPADLDQALALLRKAERPVIVLGSEASRTARKTALSAFVAATGVPVFADYEGLSMLSGLPDAMRGGLVQNLYSFAKADAAPDLVLMLGARFGLNTGHGSGQLIPHSAQVIQVDPDACELGRLQGIALGIVADVGGTIEALAQATAQDAAWPDRGDWCAKVTDLAQERYASIAAKSSSEHALHPFHASQVIAKHVDAGVTVVADGALTYLWLSEVMSRVKPGGFLCHGYLGSMGVGFGTALGAQVADLEAGRRTILVTGDGSVGYSIGEFDTLVRKQLPLIVIIMNNQSWGATLHFQQLAVGPNRVTGTRLENGSYHGVAAAFGADGYHVDSVESFSAALAQALAHNRPACINVAVALDPIPPEELI 555
                                    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       531       541       551    


Chain B from PDB  Type:PROTEIN  Length:554
 aligned with Q9F4L3_PSEFL | Q9F4L3 from UniProtKB/TrEMBL  Length:563

    Alignment length:554
                                    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       531       541       551    
         Q9F4L3_PSEFL     2 AMITGGELVVRTLIKAGVEHLFGLHGAHIDTIFQACLDHDVPIIDTRHEAAAGHAAEGYARAGAKLGVALVTAGGGFTNAVTPIANAWLDRTPVLFLTGSGALRDDETNTLQAGIDQVAMAAPITKWAHRVMATEHIPRLVMQAIRAALSAPRGPVLLDLPWDILMNQIDEDSVIIPDLVLSAHGARPDPADLDQALALLRKAERPVIVLGSEASRTARKTALSAFVAATGVPVFADYEGLSMLSGLPDAMRGGLVQNLYSFAKADAAPDLVLMLGARFGLNTGHGSGQLIPHSAQVIQVDPDACELGRLQGIALGIVADVGGTIEALAQATAQDAAWPDRGDWCAKVTDLAQERYASIAAKSSSEHALHPFHASQVIAKHVDAGVTVVADGALTYLWLSEVMSRVKPGGFLCHGYLGSMGVGFGTALGAQVADLEAGRRTILVTGDGSVGYSIGEFDTLVRKQLPLIVIIMNNQSWGATLHFQQLAVGPNRVTGTRLENGSYHGVAAAFGADGYHVDSVESFSAALAQALAHNRPACINVAVALDPIPPEELI 555
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3iaeB01 B:2-183  [code=3.40.50.970, no name defined]                                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhh...eee..hhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee...............hhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhh.....eeeeeehhhhhheee..................hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eeehhhhhhhhh..hhh.eeee.hhhhhhh.......eeeee....hhhhh...........eeeee..hhhhh.......eee..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh.....eee.........hhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh.............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee......hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iae B   2 AMITGGELVVRTLIKAGVEHLFGLHGSHIDTIFQACLDHDVPIIDTRHEAAAGHAAEGYARAGAKLGVALVTAGGGFTNAVTPIANAWLDRTPVLFLTGSGALRDDETNTLQAGIDQVAMAAPITKWAHRVMATEHIPRLVMQAIRAALSAPRGPVLLDLPWDILMNQIDEDSVIIPDLVLSAHGARPDPADLDQALALLRKAERPVIVLGSEASRTARKTALSAFVAATGVPVFADYEGLSMLSGLPDAMRGGLVQNLYSFAKADAAPDLVLMLGARFGLNTGHGSGQLIPHSAQVIQVDPDACELGRLQGIALGIVADVGGTIEALAQATAQDAAWPDRGDWCAKVTDLAQERYASIAAKSSSEHALHPFHASQVIAKHVDAGVTVVADGALTYLWLSEVMSRVKPGGFLCHGYLGSMGVGFGTALGAQVADLEAGRRTILVTGDGSVGYSIGEFDTLVRKQLPLIVIIMNNQSWGATLHFQQLAVGPNRVTGTRLENGSYHGVAAAFGADGYHVDSVESFSAALAQALAHNRPACINVAVALDPIPPEELI 555
                                    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       531       541       551
   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  (0, 0)

(no "SCOP Domain" information available for 3IAE)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IAE)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9F4L3_PSEFL | Q9F4L3)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030976    thiamine pyrophosphate binding    Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.

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  3iae
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  4.1.2.38
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 Related Entries

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UniProtKB/TrEMBL
        Q9F4L3_PSEFL | Q9F4L3: 2ag0 2ag1 2uz1 3d7k 3iaf 4qpz 4qq8

(-) Related Entries Specified in the PDB File

3iaf