PDBsum entry 3d0f

Transferase

PDB id

3d0f

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Contents

			Protein chains

					105 a.a. *

			Ligands

					PO4


					GOL

			Waters ×378

* Residue conservation analysis

PDB id:

3d0f

Links

Name:

Transferase

Title:

Structure of the big_1156.2 domain of putative penicillin-binding protein mrca from nitrosomonas europaea atcc 19718

Structure:

Penicillin-binding 1 transmembrane protein mrca. Chain: a, b. Fragment: targeted domain: residues 318-420. Synonym: peptidoglycan synthetase. Engineered: yes

Source:

Nitrosomonas europaea atcc 19718. Organism_taxid: 228410. Strain: ifo 14298. Atcc: 19718. Gene: mrca, ne2317. Expressed in: escherichia coli.

Resolution:

1.64Å

R-factor:

0.173

R-free:

0.217

Authors:

M.E.Cuff,R.Mulligan,S.Clancy,A.Joachimiak,Midwest Center For Structural Genomics (Mcsg)

Key ref:

M.E.Cuff et al. Structure of the big_1156.2 domain of putative penicillin-Binding protein mrca from nitrosomonas eur atcc 19718.. To be published, .

Date:

01-May-08

Release date:

01-Jul-08

PROCHECK

	Headers

	References

Protein chains

Q81ZZ3 (Q81ZZ3_NITEU) - Penicillin-binding protein 1A from Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)

Seq: Struc:

Seq: Struc:					770 a.a. 105 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

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



		Enzyme reactions

Enzyme class 1:

E.C.2.4.99.28 - peptidoglycan glycosyltransferase.

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

Reaction:

[GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)- di-trans,octa-cis-undecaprenyl diphosphate + beta-D-GlcNAc-(1->4)- Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa- cis-undecaprenyl diphosphate = [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D- Glu-L-Lys-D-Ala-D-Ala)](n+1)-di-trans,octa-cis-undecaprenyl diphosphate + di-trans,octa-cis-undecaprenyl diphosphate + H⁺

[GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)- di-trans,octa-cis-undecaprenyl diphosphate	+	beta-D-GlcNAc-(1->4)- Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa- cis-undecaprenyl diphosphate	=	[GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D- Glu-L-Lys-D-Ala-D-Ala)](n+1)-di-trans,octa-cis-undecaprenyl diphosphate	+	di-trans,octa-cis-undecaprenyl diphosphate	+	H(+)

Enzyme class 2:

E.C.3.4.16.4 - serine-type D-Ala-D-Ala carboxypeptidase.

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

Reaction:

D-alanyl-D-alanine + H₂O = 2 D-alanine

[GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)- di-trans,octa-cis-undecaprenyl diphosphate	+	beta-D-GlcNAc-(1->4)- Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa- cis-undecaprenyl diphosphate	=	2 × [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D- Glu-L-Lys-D-Ala-D-Ala)](n+1)-di-trans,octa-cis-undecaprenyl diphosphate

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