1F7B

CRYSTAL STRUCTURE ANALYSIS OF N-ACETYLNEURAMINATE LYASE FROM HAEMOPHILUS INFLUENZAE: CRYSTAL FORM II IN COMPLEX WITH 4-OXO-SIALIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Active site modulation in the N-acetylneuraminate lyase sub-family as revealed by the structure of the inhibitor-complexed Haemophilus influenzae enzyme.

Barbosa, J.A.R.G.Smith, B.J.DeGori, R.Ooi, H.C.Marcuccio, S.M.Campi, E.M.Jackson, W.R.Brossmer, R.Sommer, M.Lawrence, M.C.

(2000) J.Mol.Biol. 303: 405-421

  • DOI: 10.1006/jmbi.2000.4138
  • Primary Citation of Related Structures:  1F5Z, 1F6K, 1F6P, 1F73, 1F74

  • PubMed Abstract: 
  • The N-acetylneuraminate lyase (NAL) sub-family of (beta/alpha)(8) enzymes share a common catalytic step but catalyse reactions in different biological pathways. Known examples include NAL, dihydrodipicolinate synthetase (DHDPS), d-5-keto-4-deoxygluca ...

    The N-acetylneuraminate lyase (NAL) sub-family of (beta/alpha)(8) enzymes share a common catalytic step but catalyse reactions in different biological pathways. Known examples include NAL, dihydrodipicolinate synthetase (DHDPS), d-5-keto-4-deoxyglucarate dehydratase, 2-keto-3-deoxygluconate aldolase, trans-o-hydroxybenzylidenepyruvate hydrolase-aldolase and trans-2'-carboxybenzalpyruvate hydratase-aldolase. Little is known about the way in which the three-dimensional structure of the respective active sites are modulated across the sub-family to achieve cognate substrate recognition. We present here the structure of Haemophilus influenzae NAL determined by X-ray crystallography to a maximum resolution of 1.60 A, in native form and in complex with three substrate analogues (sialic acid alditol, 4-deoxy-sialic acid and 4-oxo-sialic acid). These structures reveal for the first time the mode of binding of the complete substrate in the NAL active site. On the basis of the above structures, that of substrate-complexed DHDPS and sequence comparison across the sub-family we are able to propose a unified model for active site modulation. The model is one of economy, allowing wherever appropriate the retention or relocation of residues associated with binding common substrate substituent groups. Our structures also suggest a role for the strictly conserved tyrosine residue found in all active sites of the sub-family, namely that it mediates proton abstraction by the alpha-keto acid carboxylate in a substrate-assisted catalytic reaction pathway.


    Organizational Affiliation

    Biomolecular Research Institute, 343 Royal Parade, Parkville, Victoria, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-ACETYL-NEURAMINATE LYASE
A, C
293Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)Gene Names: nanA
EC: 4.1.3.3
Find proteins for P44539 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Go to UniProtKB:  P44539
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAU
Query on NAU

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Download CCD File 
A
4,4,6,7,8,9-HEXAHYDROXY-5-METHYLCARBOXAMIDONONANOIC ACID
C11 H21 N O9
LNLFFPBOMACCNX-PRQTWWFRSA-N
 Ligand Interaction
NAV
Query on NAV

Download SDF File 
Download CCD File 
C
6,7,8,9-TETRAHYDROXY-5-METHYLCARBOXAMIDO-4-OXONONANOIC ACID
C11 H19 N O8
IZVFSUJQAOHESA-QCNRFFRDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NAVKi: 25000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 65.625α = 90.00
b = 117.990β = 90.00
c = 80.896γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALEPACKdata scaling
DENZOdata reduction
X-PLORmodel building
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance