PDBsum entry 1uux

Chelatase

PDB id: 1uux

Contents

Protein chain

161 a.a. *

Ligands

MTE

PPI

IMD

FMT

Metals

CU1

Waters ×155

* Residue conservation analysis

PDB id:

1uux

Name:

Chelatase

Title:

Structure of a molybdopterin-bound cnx1g domain links molybdenum and copper metabolism

Structure:

Molybdopterin biosynthesis cnx1. Chain: a. Fragment: g-domain, residues 462-624. Synonym: cnx1. Engineered: yes

Source:

Arabidopsis thaliana. Mouse-ear cress. Organism_taxid: 3702. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PDB file)

Resolution:

1.60Å R-factor: 0.165 R-free: 0.191

Authors:

J.Kuper,A.Llamas,H.J.Hecht,R.R.Mendel,G.Schwarz

Key ref:

J.Kuper et al. (2004). Structure of the molybdopterin-bound Cnx1G domain links molybdenum and copper metabolism. Nature, 430, 803-806. PubMed id: 15306815 DOI: 10.1038/nature02681

Date:

12-Jan-04 Release date: 09-Aug-04

Protein chain

Q39054  (CNX1_ARATH) -  Molybdopterin biosynthesis protein CNX1 from Arabidopsis thaliana

Seq: 670 a.a.

Struc: 161 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: E.C.2.10.1.1 - molybdopterin molybdotransferase.
• Reaction: adenylyl-molybdopterin + molybdate = Mo-molybdopterin + AMP + H⁺

adenylyl-molybdopterin + molybdate = Mo-molybdopterin + AMP (Bound ligand (Het Group name = MTE) matches with 74.07% similarity) + H(+)

• Cofactor: Zn(2+) or Mg(2+)
• Enzyme class 3: E.C.2.7.7.75 - molybdopterin adenylyltransferase.
• Reaction: molybdopterin + ATP + H⁺ = adenylyl-molybdopterin + diphosphate

molybdopterin + ATP + H(+) (Bound ligand (Het Group name = MTE) corresponds exactly) = adenylyl-molybdopterin + diphosphate

• Cofactor: Mn(2+) or Mg(2+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1038/nature02681

Nature 430:803-806 (2004)

PubMed id: 15306815

Structure of the molybdopterin-bound Cnx1G domain links molybdenum and copper metabolism.

J.Kuper, A.Llamas, H.J.Hecht, R.R.Mendel, G.Schwarz.

ABSTRACT

The molybdenum cofactor is part of the active site of all molybdenum-dependent enzymes, except nitrogenase. The molybdenum cofactor consists of molybdopterin, a phosphorylated pyranopterin, with an ene-dithiolate coordinating molybdenum. The same pyranopterin-based cofactor is involved in metal coordination of the homologous tungsten-containing enzymes found in archea. The molybdenum cofactor is synthesized by a highly conserved biosynthetic pathway. In plants, the multidomain protein Cnx1 catalyses the insertion of molybdenum into molybdopterin. The Cnx1 G domain (Cnx1G), whose crystal structure has been determined in its apo form, binds molybdopterin with high affinity and participates in the catalysis of molybdenum insertion. Here we present two high-resolution crystal structures of Cnx1G in complex with molybdopterin and with adenylated molybdopterin (molybdopterin-AMP), a mechanistically important intermediate. Molybdopterin-AMP is the reaction product of Cnx1G and is subsequently processed in a magnesium-dependent reaction by the amino-terminal E domain of Cnx1 to yield active molybdenum cofactor. The unexpected identification of copper bound to the molybdopterin dithiolate sulphurs in both structures, coupled with the observed copper inhibition of Cnx1G activity, provides a molecular link between molybdenum and copper metabolism.

Selected figure(s)

Figure 1.
Figure 1: Structure of the Cnx1G -MPT and Ser583Ala -MPT -AMP complexes. a, b, Ribbon representation of Cnx1G (a) and Ser583Ala (b). -Helices and -strands are shown in green and orange, respectively. Bound MPT and MPT -AMP are shown in ball-and-stick notation and are covered by the 2F[o] -F[c] electron density contoured at 1.0 . The difference density (F[o] -F[c]) is shown in red (3.5 ). c, d, Close-up views of the bound MPT (c) and AMP (d) regions in the Ser583Ala structure. e, f, Molecular surface of Ser583Ala with bound MPT -AMP showing, respectively, residues important for MPT binding (red) and catalysis12,14 (blue), and the electrostatic surface potential with 11 kT as borders for electropositive (blue) and negative (red) regions calculated with SYBIL and GRASP30. The catalytically important residues Asp 515 and Asp 548 are highlighted. The position of Mg2+ found in the homologous MoeA^22 domain is superimposed.

Figure 4.
Figure 4: Hypothetical mechanism of the molybdenum insertion reaction. The mechanism of copper chelation is unknown. Cnx1G adenylates Cu -MPT, a reaction that is thought to be cation (M2+) dependent. Cnx1E subsequently cleaves the Cu -MPT -AMP complex to activate and to transfer the molybdenum atom to MPT. The function of copper is seen in the protection of the reactive MPT dithiolate.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2004, 430, 803-806) copyright 2004.

Figures were selected by the author.