5US6

Structure of Dihydrodipicolinate Reductase from Vibrio vulnificus Bound to NADH and 2,6 Pyridine Dicarboxylic Acid with Intact Polyhistidine Tag

PDB DOI: https://doi.org/10.2210/pdb5US6/pdb

Classification: OXIDOREDUCTASE
Organism(s): Vibrio vulnificus CMCP6
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-13 Released: 2018-02-21
Deposition Author(s): Mank, N.M., Arnette, A.K., Chruszcz, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.257
R-Value Work: 0.228
R-Value Observed: 0.229

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: 386.86 kDa
Atom Count: 23,790
Modelled Residue Count: 3,159
Deposited Residue Count: 3,528
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, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	294	Vibrio vulnificus CMCP6	Mutation(s): 0 Gene Names: dapB, VV1_0567 EC: 1.17.1.8
UniProt
Find proteins for Q8DEM0 (Vibrio vulnificus (strain CMCP6)) Explore Q8DEM0 Go to UniProtKB: Q8DEM0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DEM0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain EA [auth F] SDF format, chain HA [auth G] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain QA [auth I] SDF format, chain T [auth C] SDF format, chain TA [auth J] SDF format, chain WA [auth K] MOL2 format, chain AA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth I] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth J] MOL2 format, chain WA [auth K]	AA [auth E] EA [auth F] HA [auth G] M [auth A] Q [auth B] AA [auth E], EA [auth F], HA [auth G], M [auth A], Q [auth B], QA [auth I], T [auth C], TA [auth J], WA [auth K]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain AA [auth E] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain M [auth A] Focus chain Q [auth B] Focus chain QA [auth I] Focus chain T [auth C] Focus chain TA [auth J] Focus chain WA [auth K] Interactions & Density Focus chain AA [auth E] Focus chain EA [auth F] Focus chain HA [auth G] Focus chain M [auth A] Focus chain Q [auth B] Focus chain QA [auth I] Focus chain T [auth C] Focus chain TA [auth J] Focus chain WA [auth K]
PDC Query on PDC Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain IA [auth G] SDF format, chain N [auth A] SDF format, chain PA [auth I] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain UA [auth J] SDF format, chain XA [auth K] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain PA [auth I] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth J] MOL2 format, chain XA [auth K]	BA [auth E] FA [auth F] IA [auth G] N [auth A] PA [auth I] BA [auth E], FA [auth F], IA [auth G], N [auth A], PA [auth I], R [auth B], U [auth C], UA [auth J], XA [auth K]	PYRIDINE-2,6-DICARBOXYLIC ACID C₇ H₅ N O₄ WJJMNDUMQPNECX-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain N [auth A] Focus chain PA [auth I] Focus chain R [auth B] Focus chain U [auth C] Focus chain UA [auth J] Focus chain XA [auth K] Interactions & Density Focus chain BA [auth E] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain N [auth A] Focus chain PA [auth I] Focus chain R [auth B] Focus chain U [auth C] Focus chain UA [auth J] Focus chain XA [auth K]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AB [auth L] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain GA [auth F] SDF format, chain JA [auth G] SDF format, chain KA [auth H] SDF format, chain LA [auth H] SDF format, chain MA [auth H] SDF format, chain NA [auth H] SDF format, chain O [auth A] SDF format, chain OA [auth H] SDF format, chain P [auth A] SDF format, chain RA [auth I] SDF format, chain S [auth B] SDF format, chain SA [auth I] SDF format, chain V [auth C] SDF format, chain VA [auth J] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain YA [auth K] SDF format, chain Z [auth D] SDF format, chain ZA [auth K] MOL2 format, chain AB [auth L] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain LA [auth H] MOL2 format, chain MA [auth H] MOL2 format, chain NA [auth H] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain P [auth A] MOL2 format, chain RA [auth I] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth I] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth J] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth K] MOL2 format, chain Z [auth D] MOL2 format, chain ZA [auth K]	AB [auth L] CA [auth E] DA [auth E] GA [auth F] JA [auth G] AB [auth L], CA [auth E], DA [auth E], GA [auth F], JA [auth G], KA [auth H], LA [auth H], MA [auth H], NA [auth H], O [auth A], OA [auth H], P [auth A], RA [auth I], S [auth B], SA [auth I], V [auth C], VA [auth J], W [auth D], X [auth D], Y [auth D], YA [auth K], Z [auth D], ZA [auth K]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth L] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain O [auth A] Focus chain OA [auth H] Focus chain P [auth A] Focus chain RA [auth I] Focus chain S [auth B] Focus chain SA [auth I] Focus chain V [auth C] Focus chain VA [auth J] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain YA [auth K] Focus chain Z [auth D] Focus chain ZA [auth K] Interactions & Density Focus chain AB [auth L] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain O [auth A] Focus chain OA [auth H] Focus chain P [auth A] Focus chain RA [auth I] Focus chain S [auth B] Focus chain SA [auth I] Focus chain V [auth C] Focus chain VA [auth J] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Focus chain YA [auth K] Focus chain Z [auth D] Focus chain ZA [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.61 Å
R-Value Free: 0.257
R-Value Work: 0.228
R-Value Observed: 0.229
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.906	α = 90
b = 115.845	β = 96.1
c = 148.127	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
SCALEPACK	data scaling
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-02-21

Deposition Author(s):

Mank, N.M.

Arnette, A.K.

Chruszcz, M.

Revision History (Full details and data files)

Version 1.0: 2018-02-21
Type: Initial release
Version 1.1: 2021-06-30
Changes: Database references
Version 1.2: 2024-03-06
Changes: Data collection, Database references, Refinement description