1NHC | pdb_00001nhc

Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger

PDB DOI: https://doi.org/10.2210/pdb1NHC/pdb

Classification: HYDROLASE
Organism(s): Aspergillus niger
Expression System: Aspergillus niger
Mutation(s): No

Deposited: 2002-12-19 Released: 2003-11-25
Deposition Author(s): van Pouderoyen, G., Snijder, H.J., Benen, J.A., Dijkstra, B.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.209 (Depositor), 0.217 (DCC)
R-Value Work:
0.175 (Depositor), 0.185 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.0 of the entry. See complete history.

Literature

Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger.

van Pouderoyen, G., Snijder, H.J., Benen, J.A., Dijkstra, B.W.

(2003) FEBS Lett 554: 462-466

PubMed: 14623112 Search on PubMed
DOI: https://doi.org/10.1016/s0014-5793(03)01221-3
Primary Citation Related Structures:
1NHC

PubMed Abstract:
Endopolygalacturonase I is a processive enzyme, while the 60% sequence identical endopolygalacturonase II is not. The 1.70 A resolution crystal structure of endopolygalacturonase I reveals a narrowed substrate binding cleft. In addition, Arg96, a residue in this cleft previously shown to be critical for processivity, interacts with the substrate mimics glycerol and sulfate in several well-defined conformations in the six molecules in the asymmetric unit. From this we conclude that both Arg96 and the narrowed substrate binding cleft contribute to retaining the substrate while it moves through the active site after a cleavage event has occurred.

Organizational Affiliation

Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

Macromolecule Content

Total Structure Weight: 216.08 kDa
Atom Count: 16,429
Modeled Residue Count: 2,016
Deposited Residue Count: 2,016
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polygalacturonase I	A, B, C, D, E A, B, C, D, E, F	336	Aspergillus niger	Mutation(s): 0 EC: 3.2.1.15
UniProt
Find proteins for P26213 (Aspergillus niger) Explore P26213 Go to UniProtKB: P26213
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26213
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H	6		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G94106MV GlyCosmos: G94106MV GlyGen: G94106MV

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	3		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain HA [auth E] SDF format, chain OA [auth F] SDF format, chain V [auth C] MOL2 format, chain HA [auth E] MOL2 format, chain OA [auth F] MOL2 format, chain V [auth C] mmCIF format, chain HA [auth E] mmCIF format, chain OA [auth F] mmCIF format, chain V [auth C]	HA [auth E], OA [auth F], V [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain HA [auth E] Focus chain OA [auth F] Focus chain V [auth C] Interactions & Density Focus chain HA [auth E] Focus chain OA [auth F] Focus chain V [auth C]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain FA [auth E] SDF format, chain GA [auth E] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	AA [auth D] BA [auth D] FA [auth E] GA [auth E] J [auth A] AA [auth D], BA [auth D], FA [auth E], GA [auth E], J [auth A], K [auth A], NA [auth F], O [auth B], P [auth B], T [auth C], U [auth C]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth F] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain L [auth A] SDF format, chain LA [auth E] SDF format, chain M [auth A] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	CA [auth D] DA [auth D] IA [auth E] JA [auth E] KA [auth E] CA [auth D], DA [auth D], IA [auth E], JA [auth E], KA [auth E], L [auth A], LA [auth E], M [auth A], PA [auth F], Q [auth B], QA [auth F], R [auth B], W [auth C], X [auth C], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain L [auth A] Focus chain LA [auth E] Focus chain M [auth A] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain MA [auth E] SDF format, chain N [auth A] SDF format, chain RA [auth F] SDF format, chain S [auth B] MOL2 format, chain EA [auth D] MOL2 format, chain MA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] mmCIF format, chain EA [auth D] mmCIF format, chain MA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain RA [auth F] mmCIF format, chain S [auth B]	EA [auth D], MA [auth E], N [auth A], RA [auth F], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain MA [auth E] Focus chain N [auth A] Focus chain RA [auth F] Focus chain S [auth B] Interactions & Density Focus chain EA [auth D] Focus chain MA [auth E] Focus chain N [auth A] Focus chain RA [auth F] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.209 (Depositor), 0.217 (DCC)
R-Value Work: 0.175 (Depositor), 0.185 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.012	α = 114.32
b = 84.13	β = 98
c = 96.035	γ = 89.75

Software Package:

Software Name	Purpose
DENZO	data reduction
TRUNCATE	data reduction
EPMR	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-11-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-11-25
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-08-16
Changes: Data collection, Database references, Refinement description, Structure summary
Version 3.0: 2024-12-25
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary