PDBsum entry 1xrs

Isomerase

PDB id: 1xrs

Contents

Protein chains

516 a.a. *

212 a.a. *

Ligands

B12

PLP

5AD

* Residue conservation analysis

PDB id:

1xrs

Name:

Isomerase

Title:

Crystal structure of lysine 5,6-aminomutase in complex with plp, cobalamin, and 5'-deoxyadenosine

Structure:

D-lysine 5,6-aminomutase alpha subunit. Chain: a. Engineered: yes. D-lysine 5,6-aminomutase beta subunit. Chain: b. Engineered: yes

Source:

Clostridium sticklandii. Organism_taxid: 1511. Gene: kamde. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.80Å R-factor: 0.199 R-free: 0.262

Authors:

F.Berkovitch,E.Behshad,K.H.Tang,E.A.Enns,P.A.Frey,C.L.Drennan

Key ref:

F.Berkovitch et al. (2004). A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase. Proc Natl Acad Sci U S A, 101, 15870-15875. PubMed id: 15514022 DOI: 10.1073/pnas.0407074101

Date:

15-Oct-04 Release date: 09-Nov-04

Protein chain

E3PRJ5  (KAMD_ACESD) -  Lysine 5,6-aminomutase alpha subunit from Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF)

Seq: 519 a.a.

Struc: 516 a.a.*

Protein chain

E3PRJ4  (KAME_ACESD) -  Lysine 5,6-aminomutase beta subunit from Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF)

Seq: 262 a.a.

Struc: 212 a.a.

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

Enzyme reactions

• Enzyme class: Chains A, B: E.C.5.4.3.3 - lysine 5,6-aminomutase.
• Reaction:
  1. (3S)-3,6-diaminohexanoate = (3S,5S)-3,5-diaminohexanoate
  2. D-lysine = (2R,5S)-2,5-diaminohexanoate
• Cofactor: Cob(II)alamin; Pyridoxal 5'-phosphate

Cob(II)alamin (Bound ligand (Het Group name = B12) matches with 85.71% similarity) Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

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

reference

DOI no: 10.1073/pnas.0407074101

Proc Natl Acad Sci U S A 101:15870-15875 (2004)

PubMed id: 15514022

A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase.

F.Berkovitch, E.Behshad, K.H.Tang, E.A.Enns, P.A.Frey, C.L.Drennan.

ABSTRACT

Lysine 5,6-aminomutase is an adenosylcobalamin and pyridoxal-5'-phosphate-dependent enzyme that catalyzes a 1,2 rearrangement of the terminal amino group of dl-lysine and of l-beta-lysine. We have solved the x-ray structure of a substrate-free form of lysine-5,6-aminomutase from Clostridium sticklandii. In this structure, a Rossmann domain covalently binds pyridoxal-5'-phosphate by means of lysine 144 and positions it into the putative active site of a neighboring triosephosphate isomerase barrel domain, while simultaneously positioning the other cofactor, adenosylcobalamin, approximately 25 A from the active site. In this mode of pyridoxal-5'-phosphate binding, the cofactor acts as an anchor, tethering the separate polypeptide chain of the Rossmann domain to the triosephosphate isomerase barrel domain. Upon substrate binding and transaldimination of the lysine-144 linkage, the Rossmann domain would be free to rotate and bring adenosylcobalamin, pyridoxal-5'-phosphate, and substrate into proximity. Thus, the structure embodies a locking mechanism to keep the adenosylcobalamin out of the active site and prevent radical generation in the absence of substrate.

Selected figure(s)

Figure 1.
Fig. 1. Aminomutases in the bacterial lysine fermentation pathway. (A) 5,6-LAM and 2,3-LAM catalyze similar reactions and act on similar substrates. Both enzymes require PLP, but 5,6-LAM is AdoCbl-dependent, whereas 2,3-LAM is an AdoMet-dependent iron-sulfur enzyme. The natural substrates of 5,6-LAM include DL-lysine and -L-lysine. 2,3-LAM acts on L-lysine and does not accept D-lysine as a substrate. (B) Proposed mechanism of 5,6-LAM, modified from ref. 38. The boxed step represents the state of the enzyme observed in this study. The unboxed steps are proposed to occur while 5,6-LAM is in the hypothetical top-on conformation (see the Introduction).

Figure 5.
Fig. 5. Edge-on vs. top-on enzyme conformations. (A) Structure of the substrate-free form of 5,6-LAM with the Rossmann domain in an edge-on conformation above the TIM barrel. Protein domains and cofactors are colored as in Fig. 2 A. Arrows represent the axes of the TIM barrel and Rossmann domains. (B) Structure of substrate-bound MCM (Protein Data Bank ID code 1REQ [PDB] ) with the Rossmann domain sitting directly on top of the TIM barrel (top-on). The substrate fragment, desulfo-coenzyme A (dark blue), threads through the TIM barrel domain, effecting the closure of the TIM barrel to the more compact structure shown. The Ado moiety of AdoCbl was not observed. We propose that the substrate-bound 5,6-LAM adopts a subunit arrangement like that of substrate-bound MCM, with the Rossmann domain and AdoCbl docked directly onto the center of the TIM barrel (see Results).

Figures were selected by the author.