1M3U | pdb_00001m3u

Crystal Structure of Ketopantoate Hydroxymethyltransferase complexed the Product Ketopantoate

PDB DOI: https://doi.org/10.2210/pdb1M3U/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2002-06-30 Released: 2003-07-22
Deposition Author(s): von Delft, F., Inoue, T., Saldanha, S.A., Ottenhof, H.H., Dhanaraj, V., Witty, M., Abell, C., Smith, A.G., Blundell, T.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.193 (Depositor), 0.202 (DCC)
R-Value Work:
0.152 (Depositor), 0.164 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Structure of E. coli Ketopantoate Hydroxymethyl Transferase Complexed with Ketopantoate and Mg(2+), Solved by Locating 160 Selenomethionine Sites.

von Delft, F., Inoue, T., Saldanha, S.A., Ottenhof, H.H., Schmitzberger, F., Birch, L.M., Dhanaraj, V., Witty, M., Smith, A.G., Blundell, T.L., Abell, C.

(2003) Structure 11: 985-996

PubMed: 12906829 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(03)00158-8
Primary Citation Related Structures:
1M3U

PubMed Abstract:
We report the crystal structure of E. coli ketopantoate hydroxymethyltransferase (KPHMT) at 1.9 A resolution, in complex with its product, ketopantoate. KPHMT catalyzes the first step in the biosynthesis of pantothenate (vitamin B(5)), the precursor of coenzyme A and the acyl carrier protein cofactor. The structure of the decameric enzyme was solved by multiwavelength anomalous dispersion to locate 160 selenomethionine sites and phase 560 kDa of protein, making it the largest structure solved by this approach. KPHMT adopts the (betaalpha)(8) barrel fold and is a member of the phosphoenolpyruvate/pyruvate superfamily. The active site contains a ketopantoate bidentately coordinated to Mg(2+). Similar binding is likely for the substrate, alpha-ketoisovalerate, orienting the C3 for deprotonation.

Organizational Affiliation

Department of Biochemistry, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.

Macromolecule Content

Total Structure Weight: 284.35 kDa
Atom Count: 22,849
Modeled Residue Count: 2,620
Deposited Residue Count: 2,640
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-methyl-2-oxobutanoate hydroxymethyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	264	Escherichia coli	Mutation(s): 0 Gene Names: PANB EC: 2.1.2.11
UniProt
Find proteins for P31057 (Escherichia coli (strain K12)) Explore P31057 Go to UniProtKB: P31057
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31057
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KPL Query on KPL Download:Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain X [auth G] SDF format, chain V [auth F] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain P [auth C] SDF format, chain N [auth B] SDF format, chain L [auth A] SDF format, chain DA [auth J] SDF format, chain BA [auth I] MOL2 format, chain Z [auth H] MOL2 format, chain X [auth G] MOL2 format, chain V [auth F] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain P [auth C] MOL2 format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain DA [auth J] MOL2 format, chain BA [auth I] mmCIF format, chain Z [auth H] mmCIF format, chain X [auth G] mmCIF format, chain V [auth F] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain P [auth C] mmCIF format, chain N [auth B] mmCIF format, chain L [auth A] mmCIF format, chain DA [auth J] mmCIF format, chain BA [auth I]	BA [auth I] DA [auth J] L [auth A] N [auth B] P [auth C] BA [auth I], DA [auth J], L [auth A], N [auth B], P [auth C], R [auth D], T [auth E], V [auth F], X [auth G], Z [auth H]	KETOPANTOATE C₆ H₁₀ O₄ PKVVTUWHANFMQC-UHFFFAOYSA-N		Interactions Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth H] SDF format, chain W [auth G] SDF format, chain U [auth F] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain CA [auth J] SDF format, chain AA [auth I] MOL2 format, chain Y [auth H] MOL2 format, chain W [auth G] MOL2 format, chain U [auth F] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain CA [auth J] MOL2 format, chain AA [auth I] mmCIF format, chain Y [auth H] mmCIF format, chain W [auth G] mmCIF format, chain U [auth F] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain CA [auth J] mmCIF format, chain AA [auth I]	AA [auth I] CA [auth J] K [auth A] M [auth B] O [auth C] AA [auth I], CA [auth J], K [auth A], M [auth B], O [auth C], Q [auth D], S [auth E], U [auth F], W [auth G], Y [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.193 (Depositor), 0.202 (DCC)
R-Value Work: 0.152 (Depositor), 0.164 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.074	α = 90
b = 157.17	β = 97.44
c = 100.181	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SnB	phasing
SHARP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2003-07-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-07-22
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-04-03
Changes: Refinement description

1M3U | pdb_00001m3u

Crystal Structure of Ketopantoate Hydroxymethyltransferase complexed the Product Ketopantoate

Literature

Structure of E. coli Ketopantoate Hydroxymethyl Transferase Complexed with Ketopantoate and Mg(2+), Solved by Locating 160 Selenomethionine Sites.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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