5M6R

Human porphobilinogen deaminase in complex with reaction intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of pyrrole polymerization in human porphobilinogen deaminase.

Pluta, P.Roversi, P.Bernardo-Seisdedos, G.Rojas, A.L.Cooper, J.B.Gu, S.Pickersgill, R.W.Millet, O.

(2018) Biochim Biophys Acta Gen Subj 1862: 1948-1955

  • DOI: 10.1016/j.bbagen.2018.06.013
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Human porphobilinogen deaminase (PBGD), the third enzyme in the heme pathway, catalyzes four times a single reaction to convert porphobilinogen into hydroxymethylbilane. Remarkably, PBGD employs a single active site during the process, with a distinc ...

    Human porphobilinogen deaminase (PBGD), the third enzyme in the heme pathway, catalyzes four times a single reaction to convert porphobilinogen into hydroxymethylbilane. Remarkably, PBGD employs a single active site during the process, with a distinct yet chemically equivalent bond formed each time. The four intermediate complexes of the enzyme have been biochemically validated and they can be isolated but they have never been structurally characterized other than the apo- and holo-enzyme bound to the cofactor. We present crystal structures for two human PBGD intermediates: PBGD loaded with the cofactor and with the reaction intermediate containing two additional substrate pyrrole rings. These results, combined with SAXS and NMR experiments, allow us to propose a mechanism for the reaction progression that requires less structural rearrangements than previously suggested: the enzyme slides a flexible loop over the growing-product active site cavity. The structures and the mechanism proposed for this essential reaction explain how a set of missense mutations result in acute intermittent porphyria.


    Organizational Affiliation

    Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Derio, Bizkaia 48160, Spain. Electronic address: omillet@cicbiogune.es.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Porphobilinogen deaminase
A, B
389Homo sapiensMutation(s): 0 
Gene Names: HMBSPBGDUPS
EC: 2.5.1.61
Find proteins for P08397 (Homo sapiens)
Go to UniProtKB:  P08397
NIH Common Fund Data Resources
PHAROS  P08397
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7J8
Query on 7J8

Download CCD File 
A, B
3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid
C40 H46 N4 O16
VHZWMEJYGVBAFI-UHFFFAOYSA-N
 Ligand Interaction
EPE
Query on EPE

Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.73 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.91α = 90
b = 81.2β = 93.01
c = 79.69γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spain--

Revision History 

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2019-05-29
    Changes: Data collection, Database references