2BWN | pdb_00002bwn

5-Aminolevulinate Synthase from Rhodobacter capsulatus

• PDB DOI: https://doi.org/10.2210/pdb2BWN/pdb

• Classification: TRANSFERASE
• Organism(s): Rhodobacter capsulatus
• Mutation(s): Yes 


• Deposited: 2005-07-15 Released: 2005-09-27 
• Deposition Author(s): Astner, I., Schulze, J.O., van den Heuvel, J.J., Jahn, D., Schubert, W.-D., Heinz, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.217 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of 5-Aminolevulinate Synthase, the First Enzyme of Heme Biosynthesis, and its Link to Xlsa in Humans.

Astner, I., Schulze, J.O., Van Den Heuvel, J.J., Jahn, D., Schubert, W.-D., Heinz, D.W.

(2005) EMBO J 24: 3166

• PubMed: 16121195 
• DOI: https://doi.org/10.1038/sj.emboj.7600792
• Primary Citation Related Structures: 
  2BWN, 2BWO, 2BWP


• PubMed Abstract: 
  

  5-Aminolevulinate synthase (ALAS) is the first and rate-limiting enzyme of heme biosynthesis in humans, animals, other non-plant eukaryotes, and alpha-proteobacteria. It catalyzes the synthesis of 5-aminolevulinic acid, the first common precursor of all tetrapyrroles, from glycine and succinyl-coenzyme A (sCoA) in a pyridoxal 5'-phosphate (PLP)-dependent manner. X-linked sideroblastic anemias (XLSAs), a group of severe disorders in humans characterized by inadequate formation of heme in erythroblast mitochondria, are caused by mutations in the gene for erythroid eALAS, one of two human genes for ALAS. We present the first crystal structure of homodimeric ALAS from Rhodobacter capsulatus (ALAS(Rc)) binding its cofactor PLP. We, furthermore, present structures of ALAS(Rc) in complex with the substrates glycine or sCoA. The sequence identity of ALAS from R. capsulatus and human eALAS is 49%. XLSA-causing mutations may thus be mapped, revealing the molecular basis of XLSA in humans. Mutations are found to obstruct substrate binding, disrupt the dimer interface, or hamper the correct folding. The structure of ALAS completes the structural analysis of enzymes in heme biosynthesis.

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Organizational Affiliation: 
• Division of Structural Biology, German Research Centre for Biotechnology, Braunschweig, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 176.37 kDa 
• Atom Count: 13,428 
• Modeled Residue Count: 1,586 
• Deposited Residue Count: 1,604 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-AMINOLEVULINATE SYNTHASE	A, B, C [auth D], D [auth E]	401	Rhodobacter capsulatus	Mutation(s): 6  EC: 2.3.1.37
UniProt
Find proteins for P18079 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)) Explore P18079  Go to UniProtKB:  P18079

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], H [auth B], K [auth D], N [auth E]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
SIN	F [auth A], M [auth D], O [auth E]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
SO4	I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACY	J [auth B], L [auth D]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
FMT	P [auth E]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	G [auth A], Q [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.217 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.875	α = 90
b = 92.872	β = 90
c = 250.131	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-27 
Deposition Author(s): Astner, I., Schulze, J.O., van den Heuvel, J.J., Jahn, D., Schubert, W.-D., Heinz, D.W.

Revision History  

• Version 1.0: 2005-09-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2015-12-23
  Changes: Atomic model, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description