4PJZ | pdb_00004pjz

CRYSTAL STRUCTURE OF T4 LYSOZYME-GSS-PEPTIDE IN COMPLEX WITH TEICOPLANIN-A2-2

• PDB DOI: https://doi.org/10.2210/pdb4PJZ/pdb

• Classification: Hydrolase/Antibiotic
• Organism(s): Actinoplanes teichomyceticus, Tequatrovirus T4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-05-13 Released: 2014-09-10 
• Deposition Author(s): Han, S., Le, B.V., Hajare, H., Baxter, R.H.G., Miller, S.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

X-ray Crystal Structure of Teicoplanin A2-2 Bound to a Catalytic Peptide Sequence via the Carrier Protein Strategy.

Han, S., Le, B.V., Hajare, H.S., Baxter, R.H., Miller, S.J.

(2014) J Org Chem 79: 8550-8556

• PubMed: 25147913 
• DOI: https://doi.org/10.1021/jo501625f
• Primary Citation Related Structures: 
  4PJZ, 4PK0


• PubMed Abstract: 
  

  We report the X-ray crystal structure of a site-selective peptide catalyst moiety and teicoplanin A2-2 complex. The expressed protein ligation technique was used to couple T4 lysozyme (T4L) and a synthetic peptide catalyst responsible for the selective phosphorylation of the N-acetylglucosamine sugar in a teicoplanin A2-2 derivative. The T4L-Pmh-dPro-Aib-dAla-dAla construct was crystallized in the presence of teicoplanin A2-2. The resulting 2.3 Å resolution protein-peptide-teicoplanin complex crystal structure revealed that the nucleophilic nitrogen of N-methylimidazole in the Pmh residue is in closer proximity (7.6 Å) to the N-acetylglucosamine than the two other sugar rings present in teicoplanin (9.3 and 20.3 Å, respectively). This molecular arrangement is consistent with the observed selectivity afforded by the peptide-based catalyst when it is applied to a site-selective phosphorylation reaction involving a teicoplanin A2-2 derivative.

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Organizational Affiliation: 
• Department of Chemistry, Yale University , New Haven, Connecticut 06511, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.89 kDa 
• Atom Count: 1,613 
• Modeled Residue Count: 173 
• Deposited Residue Count: 181 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TEICOPLANIN-A2-2	A [auth B]	7	Actinoplanes teichomyceticus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme	B [auth A]	174	Tequatrovirus T4	Mutation(s): 2  Gene Names: e, T4Tp126 EC: 3.2.1.17
UniProt
Find proteins for D9IEF7 (Enterobacteria phage T4) Explore D9IEF7  Go to UniProtKB:  D9IEF7

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	F [auth B]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
GCS	C [auth B]	2-amino-2-deoxy-beta-D-glucopyranose C6 H13 N O5 MSWZFWKMSRAUBD-QZABAPFNSA-N
T55	D [auth B]	8-METHYLNONANOIC ACID C10 H20 O2 OAOABCKPVCUNKO-UHFFFAOYSA-N
PO4	G [auth B], I [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	H [auth B], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
3FG	A [auth B]	L-PEPTIDE LINKING	C8 H9 N O4		--
3MY	A [auth B]	D-PEPTIDE LINKING	C9 H10 Cl N O3		TYR
GHP	A [auth B]	D-PEPTIDE LINKING	C8 H9 N O3		--
OMY	A [auth B]	L-PEPTIDE LINKING	C9 H10 Cl N O4		TYR
AIB	B [auth A]	L-PEPTIDE LINKING	C4 H9 N O2		ALA
CCS	B [auth A]	L-PEPTIDE LINKING	C5 H9 N O4 S		CYS
DAL	B [auth A]	D-PEPTIDE LINKING	C3 H7 N O2		--
DPR	B [auth A]	D-PEPTIDE LINKING	C5 H9 N O2		--
MHS	B [auth A]	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002089	A [auth B]	TEICOPLANIN-A2-2	Glycopeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.116	α = 90
b = 63.569	β = 90
c = 138.884	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-09-10 
Deposition Author(s): Han, S., Le, B.V., Hajare, H., Baxter, R.H.G., Miller, S.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-068649

Revision History  

• Version 1.0: 2014-09-10
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 2.0: 2019-12-25
  Changes: Author supporting evidence, Polymer sequence
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Structure summary