1TWI

Crystal structure of Diaminopimelate Decarboxylase from m. jannaschii in co-complex with L-lysine

PDB DOI: https://doi.org/10.2210/pdb1TWI/pdb

Classification: LYASE
Organism(s): Methanocaldococcus jannaschii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-07-01 Released: 2004-07-27
Deposition Author(s): Rajashankar, K.R., Ray, S.S., Bonanno, J.B., Pinho, M.G., He, G., De Lencastre, H., Tomasz, A., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.202
R-Value Work: 0.157
R-Value Observed: 0.157

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor

Rajashankar, K.R., Ray, S.S., Bonanno, J.B., Pinho, M.G., He, G., De Lencastre, H., Tomasz, A., Burley, S.K.

(2002) Structure 10: 1499-1508

PubMed: 12429091 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(02)00880-8
Primary Citation of Related Structures:
1TUF, 1TWI

PubMed Abstract:
Cocrystal structures of Methanococcus jannaschii diaminopimelate decarboxylase (DAPDC) bound to a substrate analog, azelaic acid, and its L-lysine product have been determined at 2.6 A and 2.0 A, respectively. This PLP-dependent enzyme is responsible for the final step of L-lysine biosynthesis in bacteria and plays a role in beta-lactam antibiotic resistance in Staphylococcus aureus. Substrate specificity derives from recognition of the L-chiral center of diaminopimelate and a system of ionic "molecular rulers" that dictate substrate length. A coupled-enzyme assay system permitted measurement of kinetic parameters for recombinant DAPDCs and inhibition constants (K(i)) for azelaic acid (89 microM) and other substrate analogs. Implications for rational design of broad-spectrum antimicrobial agents targeted against DAPDCs of drug-resistant strains of bacterial pathogens, such as Staphylococcus aureus, are discussed.

Organizational Affiliation

Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

Macromolecule Content

Total Structure Weight: 195.66 kDa
Atom Count: 15,128
Modelled Residue Count: 1,736
Deposited Residue Count: 1,736
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate decarboxylase	A, B, C, D	434	Methanocaldococcus jannaschii	Mutation(s): 0 Gene Names: LYSA, MJ1097 EC: 4.1.1.20
UniProt
Find proteins for Q58497 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58497 Go to UniProtKB: Q58497
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q58497
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain O [auth D] SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain H [auth C] MOL2 format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain H [auth C] mmCIF format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B], H [auth C], O [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain H [auth C] Focus chain O [auth D]
LYS Query on LYS Download Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain L [auth D] SDF format, chain N [auth D] SDF format, chain M [auth D] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] mmCIF format, chain I [auth D] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D]	I [auth D] J [auth D] K [auth D] L [auth D] M [auth D] I [auth D], J [auth D], K [auth D], L [auth D], M [auth D], N [auth D]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Focus chain M [auth D] Focus chain N [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.202
R-Value Work: 0.157
R-Value Observed: 0.157
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.242	α = 90
b = 147.07	β = 97.25
c = 89.389	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-07-27

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2004-07-27
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2023-08-23
Changes: Data collection, Database references, Refinement description