1NJR | pdb_00001njr

Crystal structure of yeast ymx7, an ADP-ribose-1''-monophosphatase

PDB DOI: https://doi.org/10.2210/pdb1NJR/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2003-01-02 Released: 2004-08-17
Deposition Author(s): Kumaran, D., Eswaramoorthy, S., Studier, F.W., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.230 (Depositor), 0.227 (DCC)
R-Value Work:
0.206 (Depositor), 0.205 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structure and mechanism of ADP-ribose-1''-monophosphatase (Appr-1''-pase), a ubiquitous cellular processing enzyme

Kumaran, D., Eswaramoorthy, S., Studier, F.W., Swaminathan, S.

(2005) Protein Sci 14: 719-726

PubMed: 15722447 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1110/ps.041132005
Primary Citation Related Structures:
1NJR, 1TXZ

PubMed Abstract:
Appr-1''-pase, an important and ubiquitous cellular processing enzyme involved in the tRNA splicing pathway, catalyzes the conversion of ADP-ribose-1''monophosphate (Appr-1''-p) to ADP-ribose. The structures of the native enzyme from the yeast and its complex with ADP-ribose were determined to 1.9 A and 2.05 A, respectively. Analysis of the three-dimensional structure of this protein, selected as a target in a structural genomics project, reveals its putative function and provides clues to the catalytic mechanism. The structure of the 284-amino acid protein shows a two-domain architecture consisting of a three-layer alphabetaalpha sandwich N-terminal domain connected to a small C-terminal helical domain. The structure of Appr-1''-pase in complex with the product, ADP-ribose, reveals an active-site water molecule poised for nucleophilic attack on the terminal phosphate group. Loop-region residues Asn 80, Asp 90, and His 145 may form a catalytic triad.

Organizational Affiliation

Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.

Macromolecule Content

Total Structure Weight: 32.73 kDa
Atom Count: 2,099
Modeled Residue Count: 249
Deposited Residue Count: 284
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
32.1 kDa protein in ADH3-RCA1 intergenic region	A	284	Saccharomyces cerevisiae	Mutation(s): 10 Gene Names: YMR087W or YM9582.12 EC: 3.1.3.84
UniProt
Find proteins for Q04299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04299 Go to UniProtKB: Q04299
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04299
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XYL Query on XYL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	Xylitol C₅ H₁₂ O₅ HEBKCHPVOIAQTA-SCDXWVJYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.230 (Depositor), 0.227 (DCC)
R-Value Work: 0.206 (Depositor), 0.205 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.694	α = 90
b = 38.149	β = 112.21
c = 64.736	γ = 90

Software Package:

Software Name	Purpose
MARMAD	data collection
HKL-2000	data reduction
SOLVE	phasing
SHARP	phasing
DM	model building
CNS	refinement
MARMAD	data reduction
HKL-2000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-08-17

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2004-08-17
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2021-02-03
Changes: Structure summary
Version 1.5: 2024-11-13
Changes: Data collection, Database references, Structure summary