Pyrobaculum calidifontis 5-aminolaevulinic acid dehydratase

Experimental Data Snapshot

  • Resolution: 3.47 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report

This is version 1.6 of the entry. See complete history


Structural studies of substrate and product complexes of 5-aminolaevulinic acid dehydratase from humans, Escherichia coli and the hyperthermophile Pyrobaculum calidifontis.

Mills-Davies, N.Butler, D.Norton, E.Thompson, D.Sarwar, M.Guo, J.Gill, R.Azim, N.Coker, A.Wood, S.P.Erskine, P.T.Coates, L.Cooper, J.B.Rashid, N.Akhtar, M.Shoolingin-Jordan, P.M.

(2017) Acta Crystallogr D Struct Biol 73: 9-21

  • DOI: https://doi.org/10.1107/S2059798316019525
  • Primary Citation of Related Structures:  
    5HMS, 5HNR, 5LZL, 5MHB

  • PubMed Abstract: 

    A number of X-ray analyses of an enzyme involved in a key early stage of tetrapyrrole biosynthesis are reported. Two structures of human 5-aminolaevulinate dehydratase (ALAD), native and recombinant, have been determined at 2.8 Å resolution, showing that the enzyme adopts an octameric quaternary structure in accord with previously published analyses of the enzyme from a range of other species. However, this is in contrast to the finding that a disease-related F12L mutant of the human enzyme uniquely forms hexamers [Breinig et al. (2003), Nature Struct. Biol. 10, 757-763]. Monomers of all ALADs adopt the TIM-barrel fold; the subunit conformation that assembles into the octamer includes the N-terminal tail of one monomer curled around the (α/β) 8 barrel of a neighbouring monomer. Both crystal forms of the human enzyme possess two monomers per asymmetric unit, termed A and B. In the native enzyme there are a number of distinct structural differences between the A and B monomers, with the latter exhibiting greater disorder in a number of loop regions and in the active site. In contrast, the second monomer of the recombinant enzyme appears to be better defined and the active site of both monomers clearly possesses a zinc ion which is bound by three conserved cysteine residues. In native human ALAD, the A monomer also has a ligand resembling the substrate ALA which is covalently bound by a Schiff base to one of the active-site lysines (Lys252) and is held in place by an ordered active-site loop. In contrast, these features of the active-site structure are disordered or absent in the B subunit of the native human enzyme. The octameric structure of the zinc-dependent ALAD from the hyperthermophile Pyrobaculum calidifontis is also reported at a somewhat lower resolution of 3.5 Å. Finally, the details are presented of a high-resolution structure of the Escherichia coli ALAD enzyme co-crystallized with a noncovalently bound moiety of the product, porphobilinogen (PBG). This structure reveals that the pyrrole side-chain amino group is datively bound to the active-site zinc ion and that the PBG carboxylates interact with the enzyme via hydrogen bonds and salt bridges with invariant residues. A number of hydrogen-bond interactions that were previously observed in the structure of yeast ALAD with a cyclic intermediate resembling the product PBG appear to be weaker in the new structure, suggesting that these interactions are only optimal in the transition state.

  • Organizational Affiliation

    School of Biological Sciences, University of Southampton, Southampton SO16 1BJ, England.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Delta-aminolevulinic acid dehydratase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
338Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
Gene Names: Pcal_1709
Find proteins for A3MWV9 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
Explore A3MWV9 
Go to UniProtKB:  A3MWV9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3MWV9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth H]
BA [auth H]
CA [auth I]
DA [auth I]
EA [auth J]
AA [auth H],
BA [auth H],
CA [auth I],
DA [auth I],
EA [auth J],
FA [auth J],
GA [auth K],
HA [auth K],
IA [auth L],
JA [auth L],
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth C],
R [auth C],
S [auth D],
T [auth D],
U [auth E],
V [auth E],
W [auth F],
X [auth F],
Y [auth G],
Z [auth G]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 205.561α = 90
b = 205.561β = 90
c = 199.171γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2017-01-11
    Changes: Database references
  • Version 1.2: 2017-01-25
    Changes: Database references
  • Version 1.3: 2018-08-08
    Changes: Data collection, Database references
  • Version 1.4: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2019-07-10
    Changes: Data collection
  • Version 1.6: 2024-01-17
    Changes: Data collection, Database references, Refinement description