PDBsum entry: 2inf

Lyase

PDB id: 2inf

Contents

Protein chains

344 a.a. *

Waters ×256

* Residue conservation analysis

PDB id:

2inf

Name:

Lyase

Title:

Crystal structure of uroporphyrinogen decarboxylase from bacillus subtilis

Structure:

Uroporphyrinogen decarboxylase. Chain: a, b, c, d. Synonym: uro-d, upd. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.200 R-free: 0.251

Authors:

J.Fan,Q.Liu,Q.Hao,M.K.Teng,L.W.Niu

Key ref:

J.Fan et al. (2007). Crystal structure of uroporphyrinogen decarboxylase from Bacillus subtilis. J Bacteriol, 189, 3573-3580. PubMed id: 17122346 DOI: 10.1128/JB.01083-06

Date:

06-Oct-06 Release date: 24-Oct-06

Protein chains

P32395  (DCUP_BACSU) -  Uroporphyrinogen decarboxylase

Seq: 353 a.a.

Struc: 344 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.1.1.37 - Uroporphyrinogen decarboxylase.
• Pathway: Porphyrin Biosynthesis (later stages)
• Reaction: Uroporphyrinogen III = coproporphyrinogen + 4 CO₂

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: porphyrin biosynthetic process (1 term)
• Biochemical function: lyase activity (3 terms)

Added reference

DOI no: 10.1128/JB.01083-06

J Bacteriol 189:3573-3580 (2007)

PubMed id: 17122346

Crystal structure of uroporphyrinogen decarboxylase from Bacillus subtilis.

J.Fan, Q.Liu, Q.Hao, M.Teng, L.Niu.

ABSTRACT

Uroporphyrinogen decarboxylase (UROD) is a branch point enzyme in the biosynthesis of the tetrapyrroles. It catalyzes the decarboxylation of four acetate groups of uroporphyrinogen III to yield coproporphyrinogen III, leading to heme and chlorophyll biosynthesis. UROD is a special type of nonoxidative decarboxylase, since no cofactor is essential for catalysis. In this work, the first crystal structure of a bacterial UROD, Bacillus subtilis UROD (UROD(Bs)), has been determined at a 2.3 A resolution. The biological unit of UROD(Bs) was determined by dynamic light scattering measurements to be a homodimer in solution. There are four molecules in the crystallographic asymmetric unit, corresponding to two homodimers. Structural comparison of UROD(Bs) with eukaryotic URODs reveals a variation of two loops, which possibly affect the binding of substrates and release of products. Structural comparison with the human UROD-coproporphyrinogen III complex discloses a similar active cleft, with five invariant polar residues (Arg29, Arg33, Asp78, Tyr154, and His322) and three invariant hydrophobic residues (Ile79, Phe144, and Phe207), in UROD(Bs). Among them, Asp78 may interact with the pyrrole NH groups of the substrate, and Arg29 is a candidate for positioning the acetate groups of the substrate. Both residues may also play catalytic roles.