4K3I | pdb_00004k3i

Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of MauG, C2 Space Group

PDB DOI: https://doi.org/10.2210/pdb4K3I/pdb

Classification: OXIDOREDUCTASE
Organism(s): Paracoccus denitrificans PD1222, Paracoccus denitrificans
Expression System: Paracoccus denitrificans PD1222, Cereibacter sphaeroides
Mutation(s): No

Deposited: 2013-04-10 Released: 2013-07-10
Deposition Author(s): Yukl, E.Y., Wilmot, C.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.190 (Depositor), 0.198 (DCC)
R-Value Work:
0.144 (Depositor), 0.155 (DCC)
R-Value Observed:
0.146 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structures of MauG in complex with quinol and quinone MADH.

Yukl, E.T., Jensen, L.M., Davidson, V.L., Wilmot, C.M.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 738-743

PubMed: 23832199 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309113016539
Primary Citation Related Structures:
4K3I

PubMed Abstract:
MauG has been cocrystallized with methylamine dehydrogenase (MADH) with its TTQ cofactor in the o-quinol (TTQOQ) and quinone (TTQOX) forms and the structures of the resulting complexes have been solved. The TTQOQ structure crystallized in either space group P21 or C2, while the TTQOX structure crystallized in space group P1. The previously solved structure of MauG in complex with MADH bearing an incompletely formed TTQ cofactor (preMADH) also crystallized in space group P1, although with different unit-cell parameters. Despite the changes in crystal form, the structures are virtually identical, with only very minor changes at the protein-protein interface. The relevance of these structures with respect to the measured changes in affinity between MauG and various forms of MADH is discussed.

Organizational Affiliation

Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN 55455, USA.

Macromolecule Content

Total Structure Weight: 199.97 kDa
Atom Count: 15,344
Modeled Residue Count: 1,713
Deposited Residue Count: 1,790
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylamine utilization protein MauG	A, B	373	Paracoccus denitrificans PD1222	Mutation(s): 0 Gene Names: mauG, Pden_4736 EC: 1
UniProt
Find proteins for Q51658 (Paracoccus denitrificans (strain Pd 1222)) Explore Q51658 Go to UniProtKB: Q51658
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q51658
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylamine dehydrogenase light chain	C, E	137	Paracoccus denitrificans	Mutation(s): 0 Gene Names: mauA EC: 1.4.9.1
UniProt
Find proteins for P22619 (Paracoccus denitrificans) Explore P22619 Go to UniProtKB: P22619
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22619
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylamine dehydrogenase heavy chain	D, F	385	Paracoccus denitrificans PD1222	Mutation(s): 0 Gene Names: Pden_4730 EC: 1.4.99.3 (PDB Primary Data), 1.4.9.1 (UniProt)
UniProt
Find proteins for A1BB97 (Paracoccus denitrificans (strain Pd 1222)) Explore A1BB97 Go to UniProtKB: A1BB97
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1BB97
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	H [auth A], I [auth A], P [auth B], Q [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain S [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain S [auth B]	K [auth A], L [auth A], N [auth A], S [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain S [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain S [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain U [auth D] MOL2 format, chain U [auth D] mmCIF format, chain U [auth D]	U [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain U [auth D] Interactions & Density Focus chain U [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B]	G [auth A], O [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain O [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain R [auth B] SDF format, chain T [auth B] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B]	J [auth A], M [auth A], R [auth B], T [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain T [auth B] Interactions & Density Focus chain J [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain T [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TOQ Query on TOQ	C, E	L-PEPTIDE LINKING	C₁₁ H₁₂ N₂ O₄		TRP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.190 (Depositor), 0.198 (DCC)
R-Value Work: 0.144 (Depositor), 0.155 (DCC)
R-Value Observed: 0.146 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 346.356	α = 90
b = 55.558	β = 106.55
c = 112.548	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-07-10

Deposition Author(s):

Yukl, E.Y.

Wilmot, C.M.

Revision History (Full details and data files)

Version 1.0: 2013-07-10
Type: Initial release
Version 1.1: 2013-08-28
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection, Derived calculations
Version 1.4: 2024-11-27
Changes: Structure summary