2XQ1 | pdb_00002xq1

Crystal structure of peroxisomal catalase from the yeast Hansenula polymorpha

PDB DOI: https://doi.org/10.2210/pdb2XQ1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Ogataea angusta
Mutation(s): No

Deposited: 2010-08-31 Released: 2011-06-22
Deposition Author(s): Penya-Soler, E., Vega, M.C., Wilmanns, M., Williams, C.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.223 (Depositor), 0.223 (DCC)
R-Value Work:
0.191 (Depositor), 0.193 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structural Features of Peroxisomal Catalase from the Yeast Hansenula Polymorpha

Penya-Soler, E., Vega, M.C., Wilmanns, M., Williams, C.P.

(2011) Acta Crystallogr D Biol Crystallogr 67: 690

PubMed: 21795810 Search on PubMed
DOI: https://doi.org/10.1107/S0907444911022463
Primary Citation Related Structures:
2XQ1

PubMed Abstract:
The reactive oxygen species hydrogen peroxide is a byproduct of the β-oxidation process that occurs in peroxisomes. Since reactive oxygen species can cause serious damage to biomolecules, a number of scavengers control their intracellular levels. One such scavenger that is present in the peroxisome is the oxidoreductase catalase. In this study, the crystal structure of heterologously expressed peroxisomal catalase from the thermotolerant yeast Hansenula polymorpha has been determined at 2.9 Å resolution. H. polymorpha catalase is a typical peroxisomal catalase; it is tetrameric and is highly similar to catalases from other organisms. However, its hydrogen peroxide-degrading activity is higher than those of a number of other catalases for which structural data are available. Structural superimpositions indicate that the nature of the major channel, the path for hydrogen peroxide to the active site, varies from those seen in other catalase structures, an observation that may account for the high activity of H. polymorpha catalase.

Organizational Affiliation

Department of Structural and Quantitative Biology, Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maetzu, 28040 Madrid, Spain.

Macromolecule Content

Total Structure Weight: 937.8 kDa
Atom Count: 63,839
Modeled Residue Count: 7,860
Deposited Residue Count: 8,144
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXISOMAL CATALASE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	509	Ogataea angusta	Mutation(s): 0 EC: 1.11.1.6
UniProt
Find proteins for P30263 (Pichia angusta) Explore P30263 Go to UniProtKB: P30263
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30263
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain AA [auth L] SDF format, chain BA [auth M] SDF format, chain CA [auth N] SDF format, chain DA [auth O] SDF format, chain EA [auth P] SDF format, chain Q [auth B] SDF format, chain R [auth C] SDF format, chain S [auth D] SDF format, chain T [auth E] SDF format, chain V [auth G] SDF format, chain W [auth H] SDF format, chain X [auth I] SDF format, chain Y [auth J] SDF format, chain Z [auth K] SDF format, chain U [auth F] MOL2 format, chain AA [auth L] MOL2 format, chain BA [auth M] MOL2 format, chain CA [auth N] MOL2 format, chain DA [auth O] MOL2 format, chain EA [auth P] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth E] MOL2 format, chain V [auth G] MOL2 format, chain W [auth H] MOL2 format, chain X [auth I] MOL2 format, chain Y [auth J] MOL2 format, chain Z [auth K] MOL2 format, chain U [auth F] mmCIF format, chain AA [auth L] mmCIF format, chain BA [auth M] mmCIF format, chain CA [auth N] mmCIF format, chain DA [auth O] mmCIF format, chain EA [auth P] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth E] mmCIF format, chain V [auth G] mmCIF format, chain W [auth H] mmCIF format, chain X [auth I] mmCIF format, chain Y [auth J] mmCIF format, chain Z [auth K] mmCIF format, chain U [auth F]	AA [auth L] BA [auth M] CA [auth N] DA [auth O] EA [auth P] AA [auth L], BA [auth M], CA [auth N], DA [auth O], EA [auth P], Q [auth B], R [auth C], S [auth D], T [auth E], U [auth F], V [auth G], W [auth H], X [auth I], Y [auth J], Z [auth K]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth L] Focus chain BA [auth M] Focus chain CA [auth N] Focus chain DA [auth O] Focus chain EA [auth P] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth J] Focus chain Z [auth K] Interactions & Density Focus chain AA [auth L] Focus chain BA [auth M] Focus chain CA [auth N] Focus chain DA [auth O] Focus chain EA [auth P] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth I] Focus chain Y [auth J] Focus chain Z [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.223 (Depositor), 0.223 (DCC)
R-Value Work: 0.191 (Depositor), 0.193 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.52	α = 90
b = 196.68	β = 92.85
c = 170.85	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-06-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-22
Type: Initial release
Version 1.1: 2011-07-27
Changes: Database references, Version format compliance
Version 1.2: 2012-03-28
Changes: Other
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description