2AG0

Crystal structure of Benzaldehyde lyase (BAL)- native

External Resource: Annotation


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APF00205e2ag0A1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: DHS-like NAD/FAD-binding domainF: PF00205ECOD (1.6)
APF02775e2ag0A2 A: a/b three-layered sandwichesX: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)T: Thiamin diphosphate-binding fold (THDP-binding)F: PF02775ECOD (1.6)
APF02776e2ag0A3 A: a/b three-layered sandwichesX: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)T: Thiamin diphosphate-binding fold (THDP-binding)F: PF02776ECOD (1.6)
BPF00205e2ag0B1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: DHS-like NAD/FAD-binding domainF: PF00205ECOD (1.6)
BPF02775e2ag0B2 A: a/b three-layered sandwichesX: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)T: Thiamin diphosphate-binding fold (THDP-binding)F: PF02775ECOD (1.6)
BPF02776e2ag0B3 A: a/b three-layered sandwichesX: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)T: Thiamin diphosphate-binding fold (THDP-binding)F: PF02776ECOD (1.6)
CPF00205e2ag0C1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: DHS-like NAD/FAD-binding domainF: PF00205ECOD (1.6)
CPF02775e2ag0C2 A: a/b three-layered sandwichesX: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)T: Thiamin diphosphate-binding fold (THDP-binding)F: PF02775ECOD (1.6)
CPF02776e2ag0C3 A: a/b three-layered sandwichesX: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)T: Thiamin diphosphate-binding fold (THDP-binding)F: PF02776ECOD (1.6)
DPF00205e2ag0D1 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: DHS-like NAD/FAD-binding domainF: PF00205ECOD (1.6)
DPF02775e2ag0D2 A: a/b three-layered sandwichesX: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)T: Thiamin diphosphate-binding fold (THDP-binding)F: PF02775ECOD (1.6)
DPF02776e2ag0D3 A: a/b three-layered sandwichesX: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)T: Thiamin diphosphate-binding fold (THDP-binding)F: PF02776ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.40.50.970 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domainsCATH (4.3.0)
A3.40.50.1220 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold TPP-binding domainCATH (4.3.0)
B3.40.50.970 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domainsCATH (4.3.0)
B3.40.50.1220 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold TPP-binding domainCATH (4.3.0)
C3.40.50.970 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domainsCATH (4.3.0)
C3.40.50.1220 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold TPP-binding domainCATH (4.3.0)
D3.40.50.970 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domainsCATH (4.3.0)
D3.40.50.1220 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold TPP-binding domainCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D
PF00205Thiamine pyrophosphate enzyme, central domain (TPP_enzyme_M)Thiamine pyrophosphate enzyme, central domainThe central domain of TPP enzymes contains a 2-fold Rossman fold.Domain
A, B, C, D
PF02775Thiamine pyrophosphate enzyme, C-terminal TPP binding domain (TPP_enzyme_C)Thiamine pyrophosphate enzyme, C-terminal TPP binding domain- Domain
A, B, C, D
PF02776Thiamine pyrophosphate enzyme, N-terminal TPP binding domain (TPP_enzyme_N)Thiamine pyrophosphate enzyme, N-terminal TPP binding domain- Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C, D
benzaldehyde lyase -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C, D
IPR045229Thiamine pyrophosphate enzymeFamily
A, B, C, D
IPR012001Thiamine pyrophosphate enzyme, N-terminal TPP-binding domainDomain
A, B, C, D
IPR012000Thiamine pyrophosphate enzyme, central domainDomain
A, B, C, D
IPR029035DHS-like NAD/FAD-binding domain superfamilyHomologous Superfamily
A, B, C, D
IPR029061Thiamin diphosphate-binding foldHomologous Superfamily
A, B, C, D
IPR011766Thiamine pyrophosphate enzyme, TPP-bindingDomain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

ChainsEnzyme NameDescriptionCatalytic Residues
A, B
benzoin aldolase  M-CSA #221

Thiamine diphosphate dependent benzaldehyde lyase (BAL) from Pseudomonas fluorescens catalyses the cleavage of (R)-benzoin producing two molecules of benzaldehyde. This allows the bacterium to grow on (R)-benzoin as its only carbon and energy source.

The reverse reaction is catalysed by benzoylformate decarboxylase (BFD). The X-ray structure of BAL was compared to that of BFD and pyruvate decarboxylase (PDC) in order to determine which residues are likely to have catalytic roles and should be analysed by point mutations.

BAL looses its catalytic activity upon treatment with EDTA but activity can be restored by addition of 1millimolar MgCl2, MnSO4 or CaSO4.

Defined by 4 residues: GLY:A-419HIS:B-29GLU:B-50GLN:B-113
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Explore in 3D: M-CSA Motif Definition
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EC: 4.1.2.38 (PDB Primary Data)