2Z87 | pdb_00002z87

Crystal structure of chondroitin polymerase from Escherichia coli strain K4 (K4CP) complexed with UDP-GalNAc and UDP

PDB DOI: https://doi.org/10.2210/pdb2Z87/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-09-03 Released: 2008-09-16
Deposition Author(s): Osawa, T., Sugiura, N., Shimada, H., Hirooka, R., Tsuji, A., Kimura, M., Kimata, K., Kakuta, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.283 (Depositor), 0.277 (DCC)
R-Value Work:
0.199 (Depositor), 0.198 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of chondroitin polymerase from Escherichia coli K4.

Osawa, T., Sugiura, N., Shimada, H., Hirooka, R., Tsuji, A., Shirakawa, T., Fukuyama, K., Kimura, M., Kimata, K., Kakuta, Y.

(2009) Biochem Biophys Res Commun 378: 10-14

PubMed: 18771653 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2008.08.121
Primary Citation Related Structures:
2Z86, 2Z87

PubMed Abstract:
Elongation of glycosaminoglycan chains, such as heparan and chondroitin, is catalyzed by bi-functional glycosyltransferases, for which both 3-dimensional structures and reaction mechanisms remain unknown. The bacterial chondroitin polymerase K4CP catalyzes elongation of the chondroitin chain by alternatively transferring the GlcUA and GalNAc moiety from UDP-GlcUA and UDP-GalNAc to the non-reducing ends of the chondroitin chain. Here, we have determined the crystal structure of K4CP in the presence of UDP and UDP-GalNAc as well as with UDP and UDP-GlcUA. The structures consisted of two GT-A fold domains in which the two active sites were 60A apart. UDP-GalNAc and UDP-GlcUA were found at the active sites of the N-terminal and C-terminal domains, respectively. The present K4CP structures have provided the structural basis for further investigating the molecular mechanism of biosynthesis of chondroitin chain.

Organizational Affiliation

Laboratory of Structural Biology, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka 812-8581, Japan.

Macromolecule Content

Total Structure Weight: 146.49 kDa
Atom Count: 9,983
Modeled Residue Count: 1,192
Deposited Residue Count: 1,248
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chondroitin synthase	A, B	624	Escherichia coli	Mutation(s): 0 Gene Names: kfoC EC: 2.4.1.175 (PDB Primary Data), 2.4.1.226 (PDB Primary Data)
UniProt
Find proteins for Q8L0V4 (Escherichia coli) Explore Q8L0V4 Go to UniProtKB: Q8L0V4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8L0V4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UD2 Query on UD2 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE C₁₇ H₂₇ N₃ O₁₇ P₂ LFTYTUAZOPRMMI-NESSUJCYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], I [auth B], J [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.283 (Depositor), 0.277 (DCC)
R-Value Work: 0.199 (Depositor), 0.198 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.371	α = 90
b = 109.285	β = 103.47
c = 85.575	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SnB	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-09-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-09-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-01-17
Changes: Advisory, Database references
Version 1.3: 2024-03-13
Changes: Advisory, Data collection, Database references, Derived calculations