5G5G

Escherichia coli Periplasmic Aldehyde Oxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acschembio.6b00572
  • Primary Citation of Related Structures:  
    5G5G, 5G5H

  • 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 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

    UCIBIO/Requimte, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa , 2829-516 Caparica, Portugal.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE XANTHINE DEHYDROGENASE YAGT IRON-SULFUR-BINDING SUBUNIT229Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P77165 (Escherichia coli (strain K12))
Explore P77165 
Go to UniProtKB:  P77165
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77165
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE XANTHINE DEHYDROGENASE YAGR MOLYBDENUM-BINDING SU SUBUNIT318Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P77324 (Escherichia coli (strain K12))
Explore P77324 
Go to UniProtKB:  P77324
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77324
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE XANTHINE DEHYDROGENASE YAGS FAD-BINDING SUBUNIT732Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P77489 (Escherichia coli (strain K12))
Explore P77489 
Go to UniProtKB:  P77489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP77489
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
O [auth B]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MCN
Query on MCN

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Y [auth C]PTERIN CYTOSINE DINUCLEOTIDE
C19 H22 N8 O13 P2 S2
RBWYFPNWTRZKKZ-LOIMWUFNSA-N
SF4
Query on SF4

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N [auth B]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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D [auth A],
E [auth A]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MOS
Query on MOS

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Z [auth C]DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
IOD
Query on IOD

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AA [auth C]
BA [auth C]
CA [auth C]
F [auth A]
M [auth A]
AA [auth C],
BA [auth C],
CA [auth C],
F [auth A],
M [auth A],
P [auth B],
W [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL
Query on GOL

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JA [auth C]
K [auth A]
KA [auth C]
L [auth A]
U [auth B]
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
U [auth B],
V [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

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HA [auth C],
IA [auth C],
J [auth A],
T [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

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DA [auth C]
EA [auth C]
FA [auth C]
G [auth A]
GA [auth C]
DA [auth C],
EA [auth C],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
I [auth A],
LA [auth C],
Q [auth B],
R [auth B],
S [auth B],
X [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
C
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.681α = 90
b = 78.342β = 99.69
c = 151.909γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Structure summary
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description