PDBsum entry 1m32

Transferase

PDB id

1m32

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Contents

			Protein chains

					(+ 0 more) 361 a.a. *

			Ligands

					PLP ×6


					POA ×2


					PO4 ×4

			Waters ×3040

* Residue conservation analysis

PDB id:

1m32

Links

Name:

Transferase

Title:

Crystal structure of 2-aminoethylphosphonate transaminase

Structure:

2-aminoethylphosphonate-pyruvate aminotransferase. Chain: a, b, c, d, e, f. Synonym: aep-transaminase. Engineered: yes

Source:

Salmonella typhimurium. Organism_taxid: 602. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å

R-factor:

0.166

R-free:

0.200

Authors:

C.C.H.Chen,H.Zhang,A.D.Kim,A.Howard,G.M.Sheldrick,D.Mariano-Dunnaway, O.Herzberg

Key ref:

C.C.Chen et al. (2002). Degradation pathway of the phosphonate ciliatine: crystal structure of 2-aminoethylphosphonate transaminase. Biochemistry, 41, 13162-13169. PubMed id: 12403617 DOI: 10.1021/bi026231v

Date:

26-Jun-02

Release date:

20-Nov-02

PROCHECK

	Headers

	References

Protein chains

P96060 (PHNW_SALTY) - 2-aminoethylphosphonate--pyruvate transaminase from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

Seq: Struc:					367 a.a. 361 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.2.6.1.37 - 2-aminoethylphosphonate--pyruvate transaminase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

(2-aminoethyl)phosphonate + pyruvate = phosphonoacetaldehyde + L-alanine

(2-aminoethyl)phosphonate

pyruvate

phosphonoacetaldehyde
Bound ligand (Het Group name = POA)
corresponds exactly

L-alanine

Cofactor:

Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 87.50% similarity

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

reference

DOI no: 10.1021/bi026231v	Biochemistry 41:13162-13169 (2002)
PubMed id: 12403617

Degradation pathway of the phosphonate ciliatine: crystal structure of 2-aminoethylphosphonate transaminase.
C.C.Chen, H.Zhang, A.D.Kim, A.Howard, G.M.Sheldrick, D.Mariano-Dunaway, O.Herzberg.

ABSTRACT

Phosphonates allow certain organisms to thrive in otherwise hostile environments, and 2-aminoethylphosphonate (AEP) is a precursor of many cellular phosphonates. AEP transaminase (AEPT) is an enzyme essential to phosphonate synthesis and degradation pathways. The crystal structure of AEP transaminase was determined by multiwavelength anomalous diffraction of 66 selenium atoms. The refined structure at 2.2 A resolution revealed an overall fold and active site location similar to those of the dimeric, two-domain structure of type I aminotransferases. The active site contains a cofactor, pyridoxal 5'-phosphate (PLP), and the product phosphonoacetaldehyde. Comparison with other type I aminotransferase structures shows that the PLP-protein interactions are conserved. Modeling of bound substrates and products reveals the structural basis for AEP recognition and the stereospecificity of proton elimination at the alpha-carbon and indicates conformational changes along the reaction pathway.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21460451

N.S.Pannu, W.J.Waterreus, P.Skubák, I.Sikharulidze, J.P.Abrahams, and R.A.de Graaff (2011).
Recent advances in the CRANK software suite for experimental phasing.

Acta Crystallogr D Biol Crystallogr, 67, 331-337.

20693694

H.Xu (2010).
Enhancing MAD F(A) data for substructure determination.

Acta Crystallogr D Biol Crystallogr, 66, 945-949.

20606258

P.Skubák, W.J.Waterreus, and N.S.Pannu (2010).
Multivariate phase combination improves automated crystallographic model building.

Acta Crystallogr D Biol Crystallogr, 66, 783-788.

20179338

T.C.Terwilliger (2010).
Rapid model building of alpha-helices in electron-density maps.

Acta Crystallogr D Biol Crystallogr, 66, 268-275.

20179339

T.C.Terwilliger (2010).
Rapid model building of beta-sheets in electron-density maps.

Acta Crystallogr D Biol Crystallogr, 66, 276-284.

20179340

T.C.Terwilliger (2010).
Rapid chain tracing of polypeptide backbones in electron-density maps.

Acta Crystallogr D Biol Crystallogr, 66, 285-294.

19011069

A.I.Martínez-Gómez, S.Martínez-Rodríguez, J.Pozo-Dengra, D.Tessaro, S.Servi, J.M.Clemente-Jiménez, F.Rodríguez-Vico, and F.J.Las Heras-Vázquez (2009).
Potential application of N-carbamoyl-beta-alanine amidohydrolase from Agrobacterium tumefaciens C58 for beta-amino acid production.

Appl Environ Microbiol, 75, 514-520.

19465773

T.C.Terwilliger, P.D.Adams, R.J.Read, A.J.McCoy, N.W.Moriarty, R.W.Grosse-Kunstleve, P.V.Afonine, P.H.Zwart, and L.W.Hung (2009).
Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard.

Acta Crystallogr D Biol Crystallogr, 65, 582-601.

19489722

W.W.Metcalf, and W.A.van der Donk (2009).
Biosynthesis of phosphonic and phosphinic acid natural products.

Annu Rev Biochem, 78, 65-94.

18219117

H.Xu, and C.M.Weeks (2008).
Rapid and automated substructure solution by Shake-and-Bake.

Acta Crystallogr D Biol Crystallogr, 64, 172-177.

17989071

Y.Yoshikane, N.Yokochi, M.Yamasaki, K.Mizutani, K.Ohnishi, B.Mikami, H.Hayashi, and T.Yagi (2008).
Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti MAFF303099.

J Biol Chem, 283, 1120-1127.

PDB codes:

2z9u 2z9v 2z9w 2z9x

17300176

S.Lima, R.Khristoforov, C.Momany, and R.S.Phillips (2007).
Crystal structure of Homo sapiens kynureninase.

Biochemistry, 46, 2735-2744.

PDB code:

2hzp

16751609

S.S.Rizk, M.J.Cuneo, and H.W.Hellinga (2006).
Identification of cognate ligands for the Escherichia coli phnD protein product and engineering of a reagentless fluorescent biosensor for phosphonates.

Protein Sci, 15, 1745-1751.

15983421

H.Xu, C.M.Weeks, and H.A.Hauptman (2005).
Optimizing statistical Shake-and-Bake for Se-atom substructure determination.

Acta Crystallogr D Biol Crystallogr, 61, 976-981.

16301796

P.Skubák, S.Ness, and N.S.Pannu (2005).
Extending the resolution and phase-quality limits in automated model building with iterative refinement.

Acta Crystallogr D Biol Crystallogr, 61, 1626-1635.

12832760

T.C.Terwilliger (2003).
Improving macromolecular atomic models at moderate resolution by automated iterative model building, statistical density modification and refinement.

Acta Crystallogr D Biol Crystallogr, 59, 1174-1182.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.