4JAX | pdb_00004jax

Crystal structure of dimeric KlHxk1 in crystal form X

PDB DOI: https://doi.org/10.2210/pdb4JAX/pdb

Classification: TRANSFERASE
Organism(s): Kluyveromyces lactis NRRL Y-1140
Expression System: Kluyveromyces lactis
Mutation(s): No

Deposited: 2013-02-19 Released: 2013-05-01
Deposition Author(s): Kuettner, E.B., Strater, N., Kettner, K., Otto, A., Lilie, H., Golbik, R.P., Kriegel, T.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.240 (Depositor), 0.239 (DCC)
R-Value Work:
0.200 (Depositor), 0.199 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

In vivo phosphorylation and in vitro autophosphorylation-inactivation of Kluyveromyces lactis hexokinase KlHxk1.

Kettner, K., Kuettner, E.B., Otto, A., Lilie, H., Golbik, R.P., Strater, N., Kriegel, T.M.

(2013) Biochem Biophys Res Commun 435: 313-318

PubMed: 23583397 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2013.03.121
Primary Citation Related Structures:
4JAX

PubMed Abstract:
The bifunctional hexokinase KlHxk1 is a key component of glucose-dependent signal transduction in Kluyveromyces lactis. KlHxk1 is phosphorylated in vivo and undergoes ATP-dependent autophosphorylation-inactivation in vitro. This study identifies serine-15 as the site of in vivo phosphorylation and serine-157 as the autophosphorylation-inactivation site. X-ray crystallography of the in vivo phosphorylated enzyme indicates the existence of a ring-shaped symmetrical homodimer carrying two phosphoserine-15 residues. In contrast, small-angle X-ray scattering and equilibrium sedimentation analyses reveal the existence of monomeric phosphoserine-15 KlHxk1 in solution. While phosphorylation at serine-15 and concomitant homodimer dissociation are likely to be involved in glucose signalling, mechanism and putative physiological significance of KlHxk1 inactivation by autophosphorylation at serine-157 remain to be established.

Organizational Affiliation

Institute of Physiological Chemistry, Carl Gustav Carus Medical Faculty, Technische Universität Dresden, Dresden, Germany. karina.kettner@tu-dresden.de

Macromolecule Content

Total Structure Weight: 324.86 kDa
Atom Count: 22,473
Modeled Residue Count: 2,821
Deposited Residue Count: 2,910
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexokinase	A, B, C, D, E A, B, C, D, E, F	485	Kluyveromyces lactis NRRL Y-1140	Mutation(s): 0 Gene Names: KLLA0D11352g, RAG5 EC: 2.7.1.1
UniProt
Find proteins for P33284 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)) Explore P33284 Go to UniProtKB: P33284
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33284
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain EA [auth F] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E]	AA [auth E] BA [auth E] EA [auth F] G [auth A] H [auth A] AA [auth E], BA [auth E], EA [auth F], G [auth A], H [auth A], I [auth A], J [auth A], M [auth B], O [auth C], P [auth C], Q [auth C], R [auth C], U [auth D], V [auth D], W [auth D], X [auth D], Z [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain EA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain EA [auth F] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain Y [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain CA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D]	CA [auth E] DA [auth E] K [auth A] L [auth A] N [auth B] CA [auth E], DA [auth E], K [auth A], L [auth A], N [auth B], S [auth C], T [auth C], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain DA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.240 (Depositor), 0.239 (DCC)
R-Value Work: 0.200 (Depositor), 0.199 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.81	α = 90
b = 178.3	β = 90
c = 216.21	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-05-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-05-01
Type: Initial release
Version 1.1: 2013-06-19
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-09
Changes: Structure summary

4JAX | pdb_00004jax

Crystal structure of dimeric KlHxk1 in crystal form X

Literature

In vivo phosphorylation and in vitro autophosphorylation-inactivation of Kluyveromyces lactis hexokinase KlHxk1.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Biological Assembly 6

Biological Assembly 7

Biological Assembly 8

Biological Assembly 9

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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