PDB-9qiz: Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase from P. ...

ID or keywords:

Entry

Database: PDB / ID: 9qiz

Title

Crystal Structure of S-Adenosyl-L-Homocysteine Hydrolase from P. aeruginosa: F324A Mutant Complexed with Adenosine and Rubidium Ions Replacing Native Potassium

Components

Adenosylhomocysteinase

Keywords

HYDROLASE / Protein dynamics / metal binding site disruption / anomalous data / ion coordination / SAHase / AHCY

Function / homology

Function and homology information

L-homocysteine biosynthetic process / adenosylhomocysteinase / adenosylhomocysteinase activity / L-methionine cycle / one-carbon metabolic process / cytosol
Similarity search - Function

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.06 Å

Authors

Malecki, P.H. / Wozniak, K. / Stepniewska, M. / Brzezinski, K.

Funding support

Poland, 1items

Citation

Journal: To Be Published
Title: Crystal structure of the S-adenosyl-L-homocysteine hydrolase from P. aeruginosa, a Q65N mutant probed with rubidium to prove disruption of a potassium binding site.
Authors: Malecki, P.H. / Wozniak, K. / Stepniewska, M. / Brzezinski, K.

History

Deposition	Mar 18, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 8, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9qiz.cif.gz	886.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9qiz.ent.gz	610.9 KB	Display	PDB format
PDBx/mmJSON format	9qiz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qi/9qiz ftp://data.pdbj.org/pub/pdb/validation_reports/qi/9qiz	HTTPS FTP

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Related structure data

Related structure data	9qiyC 9qj0C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#118 - Oct 2009 Sodium-Potassium Pump similarity (1) #265 - Jan 2022 Golgi Casein Kinase similarity (1)

Deposited unit

A: Adenosylhomocysteinase

B: Adenosylhomocysteinase

C: Adenosylhomocysteinase

D: Adenosylhomocysteinase

hetero molecules

211 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	74.550, 132.549, 99.397
Angle α, β, γ (deg.)	90.000, 102.056, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase Mass: 51735.031 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: ahcY, sahH, PA0432 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RILP / References: UniProt: Q9I685, adenosylhomocysteinase

#1: Protein

Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase

Mass: 51735.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa PAO1 (bacteria) / Gene: ahcY, sahH, PA0432 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RILP / References: UniProt: Q9I685, adenosylhomocysteinase

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Non-polymers , 5 types, 1175 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-ADN / ADENOSINE Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-RB / RUBIDIUM ION Mass: 85.468 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Rb
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1159 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 mM KH2PO4, 20% (w/v) PEG8000, 20% (v/v) glycerol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.2 / Wavelength: 0.81301 Å

Detector

Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 11, 2021

Radiation

Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.81301 Å / Relative weight: 1

Reflection

Resolution: 2.06→48.6 Å / Num. obs: 218880 / % possible obs: 94.5 % / Redundancy: 2.15 % / B_iso Wilson estimate: 27.64 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.076 / R_rim(I) all: 0.107 / Net I/σ(I): 5.92

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2.06-2.18	0.411	7443	0.671	0.581	1
2.18-2.33	0.296	7493	0.812	0.419	1
2.33-2.52	0.241	7205	0.839	0.341	1
2.52-2.76	0.161	6841	0.927	0.227	1
2.76-3.08	0.08	5731	0.983	0.114	1
3.08-3.55	0.054	5527	0.993	0.076	1
3.55-4.35	0.034	4418	0.996	0.049	1
4.35-6.12	0.031	3375	0.997	0.043	1
6.12-48.6	0.023	1848	0.999	0.033	1

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Processing

Software

Name	Version	Classification
PHENIX	1.21_5207	refinement
XDS		data scaling
XDS		data reduction
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.06→48.6 Å / SU ML: 0.2669 / Cross valid method: FREE R-VALUE / σ(F): 0.92 / Phase error: 29.8804
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2288	1968	0.9 %
R_work	0.1932	216668	-
obs	0.1935	218636	94.46 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 40.19 Å²

Refinement step

Cycle: LAST / Resolution: 2.06→48.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14203	0	276	1159	15638

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0025	14897
X-RAY DIFFRACTION	f_angle_d	0.5357	20222
X-RAY DIFFRACTION	f_chiral_restr	0.0434	2280
X-RAY DIFFRACTION	f_plane_restr	0.0034	2590
X-RAY DIFFRACTION	f_dihedral_angle_d	13.9162	5750

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.06-2.11	0.3937	113	0.3427	12503	X-RAY DIFFRACTION	76.12
2.11-2.16	0.3466	144	0.3121	15987	X-RAY DIFFRACTION	97.97
2.16-2.23	0.3696	142	0.2935	15913	X-RAY DIFFRACTION	97.37
2.23-2.3	0.2738	143	0.2672	15945	X-RAY DIFFRACTION	96.89
2.3-2.38	0.2986	141	0.2574	15659	X-RAY DIFFRACTION	95.75
2.38-2.48	0.2666	146	0.2314	16140	X-RAY DIFFRACTION	98.23
2.48-2.59	0.2426	147	0.2228	16026	X-RAY DIFFRACTION	97.83
2.59-2.73	0.2533	148	0.2125	16049	X-RAY DIFFRACTION	98.11
2.73-2.9	0.2305	144	0.2086	15953	X-RAY DIFFRACTION	97.37
2.9-3.12	0.2529	139	0.1979	15406	X-RAY DIFFRACTION	94.05
3.12-3.44	0.2325	144	0.1767	15710	X-RAY DIFFRACTION	95.81
3.44-3.93	0.2176	142	0.1486	15359	X-RAY DIFFRACTION	93.61
3.93-4.95	0.1524	134	0.1321	14733	X-RAY DIFFRACTION	90.03
4.95-48.6	0.1664	141	0.1546	15285	X-RAY DIFFRACTION	93.33

Refinement TLS params.

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

ID	L11 (°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)
1	2.06881610097	0.62512502062	0.600667304591	1.8458306239	0.831549725654	1.1983049233	0.0809192531583	0.0661300372401	-0.365029693686	-0.0821309560732	0.0427128584809	-0.16526187437	0.296748234604	0.0968209166361	-0.125483168345	0.782846941417	0.00632716994545	-0.0598498049939	0.312847613618	-0.0593422638092	0.31434917409	21.5368038484	-2.11606219287	13.8393973522
2	2.55357676602	-0.428773777585	0.812043113621	0.259624756175	0.207496920799	0.725682858418	0.0940905032094	-0.436837887733	-0.253661475448	0.129375023147	0.0754474045589	-0.111506115495	0.105723255626	-0.0151741967902	-0.190169951853	0.911882074832	-0.0339122068391	-0.121976675482	0.368314218201	0.0266137339104	0.316124656569	11.5702585618	3.52769322133	27.1840427668
3	0.560380202242	0.259883362966	0.0697598297834	0.664031897689	0.305567676312	1.63712484854	0.00576946683862	0.0503271259644	-0.150464167297	-0.0544776903167	-0.00841013028615	0.0363991308675	0.19545749424	-0.0737499528499	-0.00643791730193	0.655614106382	-0.0186724180888	-0.144382702424	0.233438225013	0.00266703330367	0.279421320268	-8.25367090495	0.188046478462	24.230000715
4	1.39012119955	-0.34845059606	-0.248859414361	2.75804955044	1.7614486534	1.13984827682	-0.02171306964	-0.121004748374	-0.0952455660388	0.305414359562	0.264748629307	-0.386879954046	0.252505219334	0.272466150521	-0.230697324959	0.609475927156	-0.00647861914044	-0.137967339378	0.360736461173	-0.0338768266544	0.291531722321	24.344127395	14.8803008462	30.4710968154
5	0.88487119449	-0.458450408125	0.394000014011	0.575792069177	0.0477658057579	1.24047918362	0.0482848197967	0.171533445475	-0.11680062447	-0.309416542714	-0.111887608274	0.0145304006854	0.0356893843464	0.0551607687826	-0.017310936106	0.807841202583	0.0216457344741	-0.182075584976	0.363050249987	-0.0671752426242	0.233626309328	-19.106873842	9.64319146965	-9.66883067173
6	1.81919178512	-0.418286086779	1.02894617957	0.291462288311	0.0355693606213	1.14316165439	-0.185583254912	0.0809129234197	0.157282026731	-0.0111820178664	-0.0365723938105	0.0697636605899	-0.340794859091	-0.022349537143	0.247936178178	0.697043652358	0.00250945433004	-0.137411705926	0.296253529925	-0.028142220185	0.265479217437	-16.0730798765	24.2234069955	-0.0726305993897
7	0.423541264271	-0.304702569597	-0.0903102338925	0.930152947573	0.591150327066	1.02234312988	-0.0151123025127	0.142088349201	0.0718233488527	-0.175797484664	0.0198182133635	-0.268652364274	-0.159964333851	0.0792347896254	-0.0084966393087	0.834089063533	-0.0197886695111	-0.101537446483	0.328846506109	0.0212332896703	0.20409466594	1.82492542064	30.7002543852	4.65998186096
8	2.1144482213	0.735802296351	0.480281333327	1.09397076915	0.222085169588	0.159177555366	-0.000177788564576	0.243854267359	-0.133350862432	-0.309868764578	0.0302414084684	-0.175174025355	-0.00465868625741	0.111042308922	-0.0206120639553	0.764827996724	-0.0146069476387	-0.0369360431696	0.338587195814	-0.00667836757595	0.229668573064	8.24311082675	19.2858313326	-2.71113522862
9	0.0573467949776	0.278249573685	0.0875414649589	0.252259032327	0.0692410715792	0.738096460136	0.040623468659	0.0683612747419	0.000633398415932	-0.160807708065	-0.0824950312028	0.185100240631	-0.122420628187	-0.170766522393	0.0455844681666	0.683506510613	0.0240596997794	-0.168143117171	0.336725043582	-0.0376574554397	0.285851667847	-32.2009879158	22.0740267089	6.1893647466
10	0.902348281516	-0.242125629553	0.153536139174	0.851716751611	-0.0271215097387	1.14483788153	-0.0565909022584	0.0778944021577	0.0774854975115	-0.143585607271	-0.0306740515889	0.160063730019	-0.140956989514	-0.211840002159	0.0864067409867	0.648339644065	0.0116491921741	-0.161341816019	0.299113947825	-0.0347145827999	0.278175358171	-26.014971864	52.6909290329	29.0047781041
11	0.430608185253	-0.0504765130265	-0.143621920856	0.65118799076	0.245708703289	0.711875250171	-0.0186245323914	0.0218238546081	0.0182673518361	-0.108164772156	-0.0497389803337	0.101892316807	-0.0407210703408	-0.173891875326	0.0585070057174	0.612709750713	-0.00751753474353	-0.147370747798	0.293461899883	-0.0166307396272	0.228154959801	-23.8826611806	33.0749617893	27.237762925
12	1.62645694518	0.301881163688	0.679999580668	0.652101938794	-0.0372734820672	0.920456956558	-0.0574672376998	-0.156916718371	0.124588491085	0.406061909741	0.17877885099	-0.0395806314291	-0.0791953405816	-0.143754681541	-0.109687011426	0.661050082375	0.0602116162138	-0.0869408248385	0.378477870204	0.000606086746153	0.208754188992	-12.0035156004	34.4519128518	60.3415989688
13	1.40199965724	-0.084749978035	1.04697073205	0.527234497155	0.365017759153	1.60975796794	-0.0556735827216	-0.316746652934	-0.0725499583391	0.141533564725	0.0733140148861	0.164354209421	0.187692525121	-0.287471242782	-0.0103565932627	0.712444378725	0.0578418786119	-0.0989175407757	0.393390237473	4.95860220578E-6	0.199755419961	-3.4270935443	19.8921378378	61.3246630411
14	0.737271098642	-0.497823536871	0.280984800606	0.521004149675	-0.0738763384513	0.945137214716	-0.132894856836	-0.1918372433	0.142439180976	0.191877712124	0.11212135419	-0.119539754445	-0.0564058288143	0.0957339364037	0.019503045709	0.707695278685	0.0222462769765	-0.177029796048	0.364208233656	-0.0388405771894	0.267553740276	4.45881182355	32.8228894206	62.6911883875
15	0.845931768453	-0.810254761882	0.757914316575	1.02180412159	-0.347930878501	1.14935885023	0.0119817444207	0.122591821297	0.0358725168351	-0.00537920183712	-0.0602317792117	-0.0563471015553	0.0956125553964	0.232475778102	0.0344879942261	0.612513692699	-0.0328018895761	-0.105847396891	0.32762937218	0.00936651488747	0.227708159628	7.81381412213	26.3884918216	46.6571027243
16	1.01262430798	-0.44080513663	-0.446636171139	0.431434003129	0.23634380021	0.888626400797	-0.060096145913	0.0815463103857	0.068666876258	-0.0537134824909	0.0389383796327	-0.0259773001918	-0.00748133597068	0.0389968888328	0.0229924436317	0.669057816114	-0.0365760892529	-0.132334648901	0.270791976448	-0.0078775590105	0.239952013909	7.9050077781	31.7272155199	27.9049328945
17	1.16653142467	-0.70108348193	-0.523670454236	1.10706452208	-0.921138253385	2.52516988104	-0.161170407228	-0.00957882344944	0.23533575838	-0.0324772084928	0.0620996603854	-0.208438780563	-0.213745586317	0.0185821440729	0.0999005145656	0.684612102886	-0.0598853601994	-0.146298331845	0.24647645764	-0.0215521362934	0.316501229155	12.4981567513	41.1339459115	29.8906093193
18	1.25146760025	-0.397433974222	-0.598583512029	0.8608435497	0.0846376782004	1.00941024002	0.00343545169736	-0.0844352967763	0.179818869304	0.0978817276296	0.0699942703751	-0.224445111807	-0.274515763735	0.193367820135	-0.077244946688	0.626841145549	-0.057747478767	-0.125762680294	0.265575258186	-0.0312652934375	0.271398526405	8.65931345009	47.7845171083	37.1992475008
19	1.42396252111	0.11336949516	-0.417171967415	2.5592333096	-1.16645414457	2.44363309339	-0.0385294310186	-0.03052271721	0.258851933528	0.146442090553	0.0104811814717	-0.212229306159	-0.575938904241	0.00449356964171	0.0351611209433	0.546297936342	-0.0115426068957	-0.140091354392	0.254623620944	-0.00963990668501	0.249098359055	1.84427112864	49.2099751145	38.7756316758
20	0.96238582373	0.551496341295	0.560188293037	0.312316638197	0.506323121032	1.42303170292	0.136672817533	-0.0228346620582	-0.283201368407	0.170582239151	0.0546985313002	-0.122476141258	0.219099563935	0.214919227612	-0.201956331765	0.705149505214	0.0536021221481	-0.12812872841	0.315647732086	-0.0173300988459	0.259482652022	9.33670055786	16.3441830599	59.8731746124
21	1.17178224195	-0.0637178712152	0.145253244758	0.692489972197	-0.324895489621	0.905229098775	0.0874123134032	-0.211604147364	-0.176247662653	0.072657200756	-0.013590947049	-0.0526451316939	0.210354840771	0.0185942888211	-0.0567159342606	0.666880723534	-0.0109808044547	-0.120228082153	0.292998305261	0.0425274201272	0.235887585353	0.497774877108	3.77501454468	43.1368325172

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 9 through 165 )	A	A	9 - 165	1 - 157
2	2	chain 'A' and (resid 166 through 215 )	A	A	166 - 215	158 - 207
3	3	chain 'A' and (resid 216 through 383 )	A	A	216 - 383	208 - 375
4	4	chain 'A' and (resid 384 through 469 )	A	A	384 - 469	376 - 461
5	5	chain 'B' and (resid 9 through 165 )	B	D	9 - 165	1 - 157
6	6	chain 'B' and (resid 166 through 215 )	B	D	166 - 215	158 - 207
7	7	chain 'B' and (resid 216 through 343 )	B	D	216 - 343	208 - 335
8	8	chain 'B' and (resid 344 through 383 )	B	D	344 - 383	336 - 375
9	9	chain 'B' and (resid 384 through 469 )	B	D	384 - 469	376 - 461
10	10	chain 'C' and (resid 6 through 215 )	C	G	6 - 215	1 - 210
11	11	chain 'C' and (resid 216 through 469 )	C	G	216 - 469	211 - 464
12	12	chain 'D' and (resid 9 through 34 )	D	J	9 - 34	1 - 26
13	13	chain 'D' and (resid 35 through 63 )	D	J	35 - 63	27 - 55
14	14	chain 'D' and (resid 64 through 165 )	D	J	64 - 165	56 - 157
15	15	chain 'D' and (resid 166 through 215 )	D	J	166 - 215	158 - 207
16	16	chain 'D' and (resid 216 through 279 )	D	J	216 - 279	208 - 271
17	17	chain 'D' and (resid 280 through 305 )	D	J	280 - 305	272 - 297
18	18	chain 'D' and (resid 306 through 343 )	D	J	306 - 343	298 - 335
19	19	chain 'D' and (resid 344 through 383 )	D	J	344 - 383	336 - 375
20	20	chain 'D' and (resid 384 through 424 )	D	J	384 - 424	376 - 416
21	21	chain 'D' and (resid 425 through 469 )	D	J	425 - 469	417 - 461

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