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- PDB-3mtg: Crystal structure of human S-adenosyl homocysteine hydrolase-like... -

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Basic information

Entry
Database: PDB / ID: 3mtg
TitleCrystal structure of human S-adenosyl homocysteine hydrolase-like 1 protein
ComponentsPutative adenosylhomocysteinase 2
KeywordsHYDROLASE / alpha/beta domain / tetramer / catalytic domain / co-factor binding domain / NAD / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of monoatomic ion transmembrane transporter activity / epithelial fluid transport / DAG and IP3 signaling / regulation of mRNA 3'-end processing / S-adenosylmethionine cycle / PLC beta mediated events / positive regulation of sodium ion transport / : / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac conduction ...regulation of monoatomic ion transmembrane transporter activity / epithelial fluid transport / DAG and IP3 signaling / regulation of mRNA 3'-end processing / S-adenosylmethionine cycle / PLC beta mediated events / positive regulation of sodium ion transport / : / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac conduction / Role of phospholipids in phagocytosis / Ion homeostasis / protein export from nucleus / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / regulation of monoatomic anion transport / VEGFR2 mediated cell proliferation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of insulin secretion / angiotensin-activated signaling pathway / response to calcium ion / one-carbon metabolic process / apical plasma membrane / endoplasmic reticulum membrane / RNA binding / extracellular exosome / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain ...Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / S-adenosylhomocysteine hydrolase-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsWisniewska, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Wisniewska, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Schutz, P. / Thorsell, A.G. / Tresaugues, L. / van der Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Schuler, H. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of human S-adenosyl homocysteine hydrolase-like 1 protein
Authors: Wisniewska, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / ...Authors: Wisniewska, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Schutz, P. / Thorsell, A.G. / Tresaugues, L. / van der Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Schuler, H.
History
DepositionApr 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative adenosylhomocysteinase 2
B: Putative adenosylhomocysteinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2804
Polymers98,9542
Non-polymers1,3272
Water2,054114
1
A: Putative adenosylhomocysteinase 2
B: Putative adenosylhomocysteinase 2
hetero molecules

A: Putative adenosylhomocysteinase 2
B: Putative adenosylhomocysteinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,5618
Polymers197,9074
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area22320 Å2
ΔGint-130 kcal/mol
Surface area65950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.240, 68.600, 90.370
Angle α, β, γ (deg.)90.00, 115.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative adenosylhomocysteinase 2 / / AdoHcyase 2 / S-adenosyl-L-homocysteine hydrolase 2 / S-adenosylhomocysteine hydrolase-like protein ...AdoHcyase 2 / S-adenosyl-L-homocysteine hydrolase 2 / S-adenosylhomocysteine hydrolase-like protein 1 / DC-expressed AHCY-like molecule


Mass: 49476.805 Da / Num. of mol.: 2 / Fragment: SAHH-like domain (unp residues 89:530) / Mutation: T508A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AHCYL1, DCAL, Irbit, XPVKONA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: O43865, adenosylhomocysteinase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M tri-sodium citrate dehydrate, 18% PEG 3350,0.1 M CHES, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MX-225 / Detector: CCD / Date: Nov 26, 2009 / Details: mirrors
RadiationMonochromator: Double Crystal Monochromator, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.64→46.625 Å / Num. obs: 30565 / Redundancy: 7.7 % / Biso Wilson estimate: 69.89 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07
Reflection shellResolution: 2.64→2.78 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.414 / Rsym value: 0.414

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
BUSTER2.9.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3gvp

3gvp


Resolution: 2.64→33.59 Å / Cor.coef. Fo:Fc: 0.9165 / Cor.coef. Fo:Fc free: 0.8688 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 628 2.08 %RANDOM
Rwork0.2033 ---
obs0.2042 30251 --
Displacement parametersBiso mean: 83.62 Å2
Baniso -1Baniso -2Baniso -3
1--2.5097 Å20 Å2-8.858 Å2
2---13.2369 Å20 Å2
3---15.7466 Å2
Refine analyzeLuzzati coordinate error obs: 1.018 Å
Refinement stepCycle: LAST / Resolution: 2.64→33.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 88 114 6792
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0168042
X-RAY DIFFRACTIONt_angle_deg1.1592472
X-RAY DIFFRACTIONt_dihedral_angle_d31712
X-RAY DIFFRACTIONt_trig_c_planes1712
X-RAY DIFFRACTIONt_gen_planes9795
X-RAY DIFFRACTIONt_it680420
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion3.36
X-RAY DIFFRACTIONt_chiral_improper_torsion8905
X-RAY DIFFRACTIONt_ideal_dist_contact79814
LS refinement shellResolution: 2.64→2.73 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2543 61 2.08 %
Rwork0.2133 2877 -
all0.2141 2938 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.09880.74460.12073.1655-2.82743.9320.2133-1.027-0.1103-0.3326-0.5353-0.09520.65520.87210.3220.16290.3602-0.13571.9060.0680.428140.369616.9813-9.053
26.12220.65564.19891.565-0.58023.13210.1992-1.12940.12520.0168-0.3831-0.2407-0.22531.20550.18390.129-0.0139-0.07451.7627-0.1080.33848.620132.3925-13.1873
31.204-0.2003-0.17992.03140.87434.61640.2832-0.26440.29150.49170.23740.0558-1.13740.83-0.52060.6811-0.18360.19330.1768-0.15110.386423.998751.875-23.8709
41.07680.134-0.17842.5436-0.84413.5776-0.122-0.612-0.0662-0.2431-0.1129-0.35960.7521.77190.2350.34470.4272-0.00491.12050.01470.357243.772323.073-31.5185
53.4141.6911-1.08479.62051.722912.5230.53280.01680.9412-1.2635-0.3701-0.84-1.97990.8315-0.16270.8876-0.33230.65360.6238-0.0680.787547.542755.9477-64.7722
62.6591-1.7446-1.87554.40610.47393.4060.5442-0.33970.5607-0.881-0.0655-1.2962-0.25041.5209-0.47860.4213-0.19940.37371.0319-0.23010.695353.227541.92-61.8483
71.5870.2166-1.29352.5896-0.15074.3392-0.28930.0244-0.1559-0.85020.1649-0.13331.49970.29290.12440.93510.11940.0250.1399-0.02830.306128.664618.8347-56.2264
81.05860.3538-0.92223.0703-0.51652.22290.3649-0.480.1480.0981-0.0019-0.7017-0.71741.876-0.3630.3752-0.39850.1771.1088-0.31690.542645.686748.1474-42.9211
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|123 - A|221 }A123 - 221
2X-RAY DIFFRACTION2{ A|222 - A|316 }A222 - 316
3X-RAY DIFFRACTION3{ A|317 - A|463 }A317 - 463
4X-RAY DIFFRACTION4{ A|464 - A|552 }A464 - 552
5X-RAY DIFFRACTION5{ B|123 - B|175 }B123 - 175
6X-RAY DIFFRACTION6{ B|176 - B|317 }B176 - 317
7X-RAY DIFFRACTION7{ B|318 - B|465 }B318 - 465
8X-RAY DIFFRACTION8{ B|466 - B|552 }B466 - 552

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