5TJZ

Structure of 4-Hydroxytetrahydrodipicolinate Reductase from Mycobacterium tuberculosis with NADPH and 2,6 Pyridine Dicarboxylic Acid

PDB DOI: https://doi.org/10.2210/pdb5TJZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis H37Ra
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-10-05 Released: 2018-01-10
Deposition Author(s): Mank, N.J., Arnette, A.K., Klapper, V., Chruszcz, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.169
R-Value Work: 0.148
R-Value Observed: 0.149

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus.

Pote, S., Kachhap, S., Mank, N.J., Daneshian, L., Klapper, V., Pye, S., Arnette, A.K., Shimizu, L.S., Borowski, T., Chruszcz, M.

(2021) Biochim Biophys Acta Gen Subj 1865: 129750-129750

PubMed: 32980502 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.bbagen.2020.129750
Primary Citation of Related Structures:
5TEJ, 5TEK, 5TEM, 5TEN, 5TJY, 5TJZ, 5UGV, 5US6

PubMed Abstract:
The products of the lysine biosynthesis pathway, meso-diaminopimelate and lysine, are essential for bacterial survival. This paper focuses on the structural and mechanistic characterization of 4-hydroxy-tetrahydrodipicolinate reductase (DapB), which is one of the enzymes from the lysine biosynthesis pathway. DapB catalyzes the conversion of (2S, 4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate (HTPA) to 2,3,4,5-tetrahydrodipicolinate in an NADH/NADPH dependent reaction. Genes coding for DapBs were identified as essential for many pathogenic bacteria, and therefore DapB is an interesting new target for the development of antibiotics.

Organizational Affiliation

Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.

Macromolecule Content

Total Structure Weight: 27.68 kDa
Atom Count: 2,331
Modelled Residue Count: 245
Deposited Residue Count: 245
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate reductase	A	245	Mycobacterium tuberculosis H37Ra	Mutation(s): 0 Gene Names: dapB, MRA_2798 EC: 1.17.1.8
UniProt
Find proteins for P9WP23 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WP23 Go to UniProtKB: P9WP23
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WP23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PDC Query on PDC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PYRIDINE-2,6-DICARBOXYLIC ACID C₇ H₅ N O₄ WJJMNDUMQPNECX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
AE3 Query on AE3 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	2-(2-ETHOXYETHOXY)ETHANOL C₆ H₁₄ O₃ XXJWXESWEXIICW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
BEZ Query on BEZ Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A]	P [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain S [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain S [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], S [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain S [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain G [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A]	G [auth A], Q [auth A], R [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain G [auth A] Focus chain Q [auth A] Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.169
R-Value Work: 0.148
R-Value Observed: 0.149
Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.157	α = 90
b = 67.157	β = 90
c = 251.325	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-01-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-01-10
Type: Initial release
Version 1.1: 2021-06-30
Changes: Database references
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

5TJZ

Structure of 4-Hydroxytetrahydrodipicolinate Reductase from Mycobacterium tuberculosis with NADPH and 2,6 Pyridine Dicarboxylic Acid

Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)