1QLM

The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from the hyperthermophilic archaeon Methanopyrus kandleri

PDB DOI: https://doi.org/10.2210/pdb1QLM/pdb

Classification: HYDROLASE
Organism(s): Methanopyrus kandleri
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1999-09-01 Released: 1999-09-20
Deposition Author(s): Grabarse, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.219
R-Value Work: 0.198
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The Crystal Structure of Methenyltetrahydromethano- Pterin Cyclohydrolase from the Hyperthermophilic Archaeon Methanopyrus Kandleri

Grabarse, W., Vaupel, M., Vorholt, J.A., Shima, S., Thauer, R.K., Wittershagen, A., Bourenkov, G., Bartunik, H.D., Ermler, U.

(1999) Structure 7: 1257

PubMed: 10545331 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(00)80059-3
Primary Citation of Related Structures:
1QLM

PubMed Abstract:
The reduction of carbon dioxide to methane in methanogenic archaea involves the tetrahydrofolate analogue tetrahydromethanopterin (H(4)MPT) as a C(1) unit carrier. In the third step of this reaction sequence, N(5)-formyl-H(4)MPT is converted to methenyl-H(4)MPT(+) by the enzyme methenyltetrahydromethanopterin cyclohydrolase. The cyclohydrolase from the hyperthermophilic archaeon Methanopyrus kandleri (Mch) is extremely thermostable and adapted to a high intracellular concentration of lyotropic salts.

Organizational Affiliation

Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Strasse, 35043, Marburg, Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Strasse 7, 60528, Frankurt, Germany.

Macromolecule Content

Total Structure Weight: 34.38 kDa
Atom Count: 2,642
Modelled Residue Count: 316
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHENYLTETRAHYDROMETHANOPTERIN CYCLOHYDROLASE	A	316	Methanopyrus kandleri	Mutation(s): 0 EC: 3.5.4.27
UniProt
Find proteins for P94954 (Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)) Explore P94954 Go to UniProtKB: P94954
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P94954
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.219
R-Value Work: 0.198
R-Value Observed: 0.198
Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.9	α = 90
b = 125.9	β = 90
c = 172.4	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1999-09-20

Deposition Author(s):

Grabarse, W.

Revision History (Full details and data files)

Version 1.0: 1999-09-20
Type: Initial release
Version 1.1: 2012-11-14
Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
Version 1.2: 2017-07-05
Changes: Data collection