PDBsum entry 1ngx

Immune system

PDB id: 1ngx

Contents

Protein chains

213 a.a. *

216 a.a. *

Ligands

JEF ×2

Waters ×672

* Residue conservation analysis

PDB id:

1ngx

Name:

Immune system

Title:

Chimeric germline fab 7g12 with jeffamine fragment bound

Structure:

Germline metal chelatase catalytic antibody, light chain. Chain: a, l. Fragment: germline fab fragment. Engineered: yes. Germline metal chelatase catalytic antibody, heavy chain. Chain: b, h. Fragment: germline fab fragment. Engineered: yes

Source:

Mus musculus, homo sapiens. House mouse, human. Organism_taxid: 10090,9606. Strain: ,. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.225 R-free: 0.250

Authors:

J.Yin,S.E.Andryski,A.B.Beuscher,R.C.Stevens,P.G.Schultz

Key ref:

J.Yin et al. (2003). Structural evidence for substrate strain in antibody catalysis. Proc Natl Acad Sci U S A, 100, 856-861. PubMed id: 12552112 DOI: 10.1073/pnas.0235873100

Date:

18-Dec-02 Release date: 18-Mar-03

Protein chains

No UniProt id for this chain

Struc: 213 a.a.

Protein chains

No UniProt id for this chain

Struc: 216 a.a.

DOI no: 10.1073/pnas.0235873100

Proc Natl Acad Sci U S A 100:856-861 (2003)

PubMed id: 12552112

Structural evidence for substrate strain in antibody catalysis.

J.Yin, S.E.Andryski, A.E.Beuscher, R.C.Stevens, P.G.Schultz.

ABSTRACT

The crystal structure of the Michaelis complex between the Fab fragment of ferrochelatase antibody 7G12 and its substrate mesoporphyrin has been solved to 2.6-A resolution. The antibody-bound mesoporphyrin clearly adopts a nonplanar conformation and reveals that the antibody catalyzes the porphyrin metallation reaction by straining/distorting the bound substrate toward the transition-state configuration. The crystal structures of the Fab fragment of the germ-line precursor antibody to 7G12 and its complex with the hapten N-methylmesoporphyrin have also been solved. A comparison of these structures with the corresponding structures of the affinity-matured antibody 7G12 reveals the molecular mechanism by which the immune system evolves binding energy to catalyze this reaction.

Selected figure(s)

Figure 2.
Fig. 2. Out-of-plane displacement of the porphyrin ring atoms from the porphyrin least-squares plane for MP (blue) and NMP (pink) bound to antibody 7G12. The porphyrin atoms that are involved in the same pyrrole ring are connected to give a pentagon shape. A-D denote the porphyrin pyrroles as in Fig. 1C, and N denotes the pyrrole nitrogen atoms of the porphyrin molecule.

Figure 4.
Fig. 4. The difference in electrostatic surface potential of the antibody-combining site in the germ-line and affinity-matured Fab and the changes upon the binding of NMP and MP. The red and blue colors correspond to negative and positive surface potential, respectively. The figure was prepared with GRASP (28).

Figures were selected by an automated process.