5CM7

Structure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP) and thiamine diphosphate (TPP)

PDB DOI: https://doi.org/10.2210/pdb5CM7/pdb

Classification: TRANSFERASE
Organism(s): Acinetobacter baumannii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-16 Released: 2015-08-26
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.167
R-Value Work: 0.142
R-Value Observed: 0.142

Starting Model: experimental
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Literature

Crystal structures of thiamine monophosphate kinase from Acinetobacter baumannii in complex with substrates and products.

Sullivan, A.H., Dranow, D.M., Horanyi, P.S., Lorimer, D.D., Edwards, T.E., Abendroth, J.

(2019) Sci Rep 9: 4392-4392

PubMed: 30867460 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41598-019-40558-x
Primary Citation of Related Structures:
5CC8, 5CM7, 5DD7, 6MFM

PubMed Abstract:
Thiamine monophosphate kinase (ThiL) catalyzes the last step of thiamine pyrophosphate (TPP) synthesis, the ATP-dependent phosphorylation of thiamine monophosphate (TMP) to thiamine pyrophosphate. We solved the structure of ThiL from the human pathogen A. baumanii in complex with a pair of substrates TMP and a non-hydrolyzable adenosine triphosphate analog, and in complex with a pair of products TPP and adenosine diphosphate. High resolution of the data and anomalous diffraction allows for a detailed description of the binding mode of substrates and products, and their metal environment. The structures further support a previously proposed in-line attack reaction mechanism and show a distinct variability of metal content of the active site.

Organizational Affiliation

UCB/Beryllium Discovery, 98110, 7869 NE Day Road West, Bainbridge Island, WA, USA.

Macromolecule Content

Total Structure Weight: 70.81 kDa
Atom Count: 5,689
Modelled Residue Count: 609
Deposited Residue Count: 626
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiamine-monophosphate kinase	A, B	313	Acinetobacter baumannii	Mutation(s): 0 Gene Names: thiL, ABUW_0092 EC: 2.7.4.16
UniProt
Find proteins for A0A0D5YC82 (Acinetobacter baumannii) Explore A0A0D5YC82 Go to UniProtKB: A0A0D5YC82
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0D5YC82
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain O [auth B]	C [auth A], O [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain O [auth B]
TPP Query on TPP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	G [auth A], K [auth B]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain P [auth B]	D [auth A] H [auth A] I [auth A] L [auth B] M [auth B] D [auth A], H [auth A], I [auth A], L [auth B], M [auth B], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth B]	E [auth A], J [auth A], N [auth B], Q [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain R [auth B] mmCIF format, chain F [auth A] mmCIF format, chain R [auth B]	F [auth A], R [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain R [auth B] Interactions & Density Focus chain F [auth A] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.167
R-Value Work: 0.142
R-Value Observed: 0.142
Space Group: P 1 2₁ 1
Diffraction Data: https://doi.org/10.18430/M35CM7

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.75	α = 90
b = 117.12	β = 108.57
c = 55.89	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-08-26

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2015-08-26
Type: Initial release
Version 1.1: 2019-03-27
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

5CM7

Structure of thiamine-monophosphate kinase from Acinetobacter baumannii in complex with adenosine diphosphate (ADP) and thiamine diphosphate (TPP)

Crystal structures of thiamine monophosphate kinase from Acinetobacter baumannii in complex with substrates and products.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)