1A7A | pdb_00001a7a

STRUCTURE OF HUMAN PLACENTAL S-ADENOSYLHOMOCYSTEINE HYDROLASE: DETERMINATION OF A 30 SELENIUM ATOM SUBSTRUCTURE FROM DATA AT A SINGLE WAVELENGTH

PDB DOI: https://doi.org/10.2210/pdb1A7A/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 1998-03-10 Released: 1999-04-20
Deposition Author(s): Turner, M.A., Yuan, C.-S., Borchardt, R.T., Hershfield, M.S., Smith, G.D., Howell, P.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.247 (Depositor), 0.249 (DCC)
R-Value Work:
0.227 (Depositor), 0.225 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure determination of selenomethionyl S-adenosylhomocysteine hydrolase using data at a single wavelength.

Turner, M.A., Yuan, C.S., Borchardt, R.T., Hershfield, M.S., Smith, G.D., Howell, P.L.

(1998) Nat Struct Biol 5: 369-376

PubMed: 9586999 Search on PubMed
DOI: https://doi.org/10.1038/nsb0598-369
Primary Citation Related Structures:
1A7A

PubMed Abstract:
S-Adenosylhomocysteine (AdoHcy) hydrolase regulates all adenosylmethionine-(AdoMet) dependent transmethylations by hydrolyzing the potent feedback inhibitor AdoHcy to homocysteine and adenosine. The crystallographic structure determination of a selenomethionyl-incorporated AdoHcy hydrolase inhibitor complex was accomplished using single wavelength anomalous diffraction data and the direct methods program, Snb v2.0, which produced the positions of all 30 crystallographically distinct selenium atoms. The mode of enzyme-cofactor binding is unique, requiring interactions from two protein monomers. An unusual dual role for a catalytic water molecule in the active site is revealed in the complex with the adenosine analog 2'-hydroxy, 3'-ketocyclopent-4'-enyladenine.

Organizational Affiliation

Structural Biology and Biochemistry, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada.

Macromolecule Content

Total Structure Weight: 98.84 kDa
Atom Count: 6,834
Modeled Residue Count: 861
Deposited Residue Count: 864
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-ADENOSYLHOMOCYSTEINE HYDROLASE	A, B	432	Homo sapiens	Mutation(s): 15 EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P23526 (Homo sapiens) Explore P23526 Go to UniProtKB: P23526
PHAROS: P23526 GTEx: ENSG00000101444
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23526
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
ADC Query on ADC Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	(1'R,2'S)-9-(2-HYDROXY-3'-KETO-CYCLOPENTEN-1-YL)ADENINE C₁₀ H₁₁ N₅ O₂ RQPALADHFYHEHK-CHKWXVPMSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.247 (Depositor), 0.249 (DCC)
R-Value Work: 0.227 (Depositor), 0.225 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.93	α = 90
b = 168.02	β = 90
c = 137.77	γ = 90

Software Package:

Software Name	Purpose
SHAKE-N-BAKE	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHAKE-N-BAKE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 1999-04-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1999-04-20
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2021-11-03
Changes: Database references, Derived calculations, Other
Version 1.4: 2024-10-23
Changes: Data collection, Structure summary