5XQO

Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with tetrameric substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26

Kunishige, Y.Iwai, M.Nakazawa, M.Ueda, M.Tada, T.Nishimura, S.Sakamoto, T.

(2018) FEBS Lett 592: 1378-1388

  • DOI: 10.1002/1873-3468.13034
  • Primary Citation of Related Structures:  
    5XQ3, 5XQG, 5XQJ, 5XQO

  • PubMed Abstract: 
  • Exo-rhamnogalacturonan lyase from Penicillium chrysogenum 31B (PcRGLX) was recently classified as a member of polysaccharide lyase (PL) family 26 along with hypothetical proteins derived from various organisms. In this study, we determined the crystal structure of PcRGLX as the first structure of a member of this family ...

    Exo-rhamnogalacturonan lyase from Penicillium chrysogenum 31B (PcRGLX) was recently classified as a member of polysaccharide lyase (PL) family 26 along with hypothetical proteins derived from various organisms. In this study, we determined the crystal structure of PcRGLX as the first structure of a member of this family. Based on the substrate-binding orientation and substrate specificity, PcRGLX is an exo-type PL that cleaves rhamnogalacturonan from the reducing end. Analysis of PcRGLX-complex structures with reaction products indicate that the active site possesses an L-shaped cleft that can accommodate galactosyl side chains, suggesting side-chain-bypassing activity in PcRGLX. Furthermore, we determined the residues critical for catalysis by analyzing the enzyme activities of inactive variants.


    Organizational Affiliation

    Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Pcrglx proteinA, B906Penicillium chrysogenumMutation(s): 1 
Gene Names: PcrglxEN45_041150
UniProt
Find proteins for B6H7Q7 (Penicillium rubens (strain ATCC 28089 / DSM 1075 / NRRL 1951 / Wisconsin 54-1255))
Explore B6H7Q7 
Go to UniProtKB:  B6H7Q7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6H7Q7
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-alpha-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranoseC 4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G02262OD
GlyCosmos:  G02262OD
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-3)-alpha-L-rhamnopyranose-(1-4)-alpha-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranoseD 4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G08304DK
GlyCosmos:  G08304DK
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.437α = 90
b = 166.437β = 90
c = 171.932γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-16
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary