5G5H

Escherichia coli Periplasmic Aldehyde Oxidase R440H mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Escherichia Coli Periplasmic Aldehyde Oxidoreductase is an Exceptional Member of the Xanthine Oxidase Family of Molybdoenzymes.

Correia, M.A.Otrelo-Cardoso, A.R.Schwuchow, V.Sigfridsson Clauss, K.G.Haumann, M.Romao, M.J.Leimkuhler, S.Santos-Silva, T.

(2016) Acs Chem.Biol. 11: 2923

  • DOI: 10.1021/acschembio.6b00572
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The xanthine oxidase (XO) family comprises molybdenum-dependent enzymes that usually form homodimers (or dimers of heterodimers/trimers) organized in three domains that harbor two [2Fe-2S] clusters, one FAD, and a Mo cofactor. In this work, we crysta ...

    The xanthine oxidase (XO) family comprises molybdenum-dependent enzymes that usually form homodimers (or dimers of heterodimers/trimers) organized in three domains that harbor two [2Fe-2S] clusters, one FAD, and a Mo cofactor. In this work, we crystallized an unusual member of the family, the periplasmic aldehyde oxidoreductase PaoABC from Escherichia coli. This is the first example of an E. coli protein containing a molybdopterin-cytosine-dinucleotide cofactor and is the only heterotrimer of the XO family so far structurally characterized. The crystal structure revealed the presence of an unexpected [4Fe-4S] cluster, anchored to an additional 40 residues subdomain. According to phylogenetic analysis, proteins containing this cluster are widely spread in many bacteria phyla, putatively through repeated gene transfer events. The active site of PaoABC is highly exposed to the surface with no aromatic residues and an arginine (PaoC-R440) making a direct interaction with PaoC-E692, which acts as a base catalyst. In order to understand the importance of R440, kinetic assays were carried out, and the crystal structure of the PaoC-R440H variant was also determined.


    Organizational Affiliation

    Freie Universität Berlin , Fachbereich Physik, 14195 Berlin, Germany.,Institut für Biologie und Biochemie, Universität Potsdam , Am Neuen Palais 10, 14469 Potsdam, Deutschland.,UCIBIO/Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE XANTHINE DEHYDROGENASE YAGT IRON-SULFUR-BINDING SUBUNIT
A
229Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: paoA (yagT)
EC: 1.2.99.6
Find proteins for P77165 (Escherichia coli (strain K12))
Go to UniProtKB:  P77165
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE XANTHINE DEHYDROGENASE YAGS FAD-BINDING SUBUNIT
B
318Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: paoB (yagS)
EC: 1.2.99.6
Find proteins for P77324 (Escherichia coli (strain K12))
Go to UniProtKB:  P77324
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE XANTHINE DEHYDROGENASE YAGR MOLYBDENUM-BINDING SUBUNIT
C
732Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: paoC (yagR)
EC: 1.2.99.6
Find proteins for P77489 (Escherichia coli (strain K12))
Go to UniProtKB:  P77489
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
IOD
Query on IOD

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A, B, C
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
MCN
Query on MCN

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C
PTERIN CYTOSINE DINUCLEOTIDE
C19 H22 N8 O13 P2 S2
RBWYFPNWTRZKKZ-LOIMWUFNSA-N
 Ligand Interaction
ACT
Query on ACT

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A, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
FAD
Query on FAD

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B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

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C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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A
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MOS
Query on MOS

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C
DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
 Ligand Interaction
CSD
Query on CSD

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C
3-SULFINOALANINE
S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE
C3 H7 N O4 S
ADVPTQAUNPRNPO-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 109.839α = 90.00
b = 78.263β = 99.93
c = 151.732γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-11-09
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Structure summary