PDB-1z6z: Crystal Structure of Human Sepiapterin Reductase in complex with NADP+

ID or keywords:

Entry

Database: PDB / ID: 1z6z

Title

Crystal Structure of Human Sepiapterin Reductase in complex with NADP+

Components

Sepiapterin reductase

Keywords

OXIDOREDUCTASE / short-chain dehydrogenase/reductase / sepiapterin reductase / human / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

sepiapterin reductase (L-erythro-7,8-dihydrobiopterin-forming) / sepiapterin reductase (NADP+) activity / aldo-keto reductase (NADPH) activity / tetrahydrobiopterin biosynthetic process / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / nitric oxide biosynthetic process / NADP binding / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Ugochukwu, E. / Kavanagh, K. / Ng, S. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC)

Citation

Journal: To be Published
Title: Crystal Structure of Human Sepiapterin Reductase
Authors: Ugochukwu, E. / Kavanagh, K. / Ng, S. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / von Delft, F. / Oppermann, U.

History

Deposition	Mar 23, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 5, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Apr 4, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4	Aug 23, 2023	Group: 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1z6z.cif.gz	303.3 KB	Display	PDBx/mmCIF format
PDB format	pdb1z6z.ent.gz	244.7 KB	Display	PDB format
PDBx/mmJSON format	1z6z.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	1z6z_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	1z6z_full_validation.pdf.gz	2.3 MB	Display
Data in XML	1z6z_validation.xml.gz	56.2 KB	Display
Data in CIF	1z6z_validation.cif.gz	75.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z6/1z6z ftp://data.pdbj.org/pub/pdb/validation_reports/z6/1z6z	HTTPS FTP

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Related structure data

Related structure data	1sepS S: Starting model for refinement
Similar structure data	6i6p-d 5nig-d 2y2i-d 2bg1-d 4j7u-2 1sep-1 2y2j-d 2k1n-d 6isn-d 6i6c-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1sepS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (6) #44 - Aug 2003 Calmodulin similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (1) #196 - Apr 2016 Lead Poisoning similarity (2) #28 - Apr 2002 Anthrax Toxin similarity (2) #206 - Feb 2017 Globin Evolution similarity (1) #34 - Oct 2002 Dihydrofolate Reductase similarity (1)

Deposited unit

A: Sepiapterin reductase

B: Sepiapterin reductase

C: Sepiapterin reductase

D: Sepiapterin reductase

E: Sepiapterin reductase

F: Sepiapterin reductase

hetero molecules

188 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Sepiapterin reductase

B: Sepiapterin reductase

hetero molecules

defined by author&software
62.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Sepiapterin reductase

D: Sepiapterin reductase

hetero molecules

defined by author&software
62.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Sepiapterin reductase

F: Sepiapterin reductase

hetero molecules

defined by author&software
62.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	55.274, 95.001, 162.825
Angle α, β, γ (deg.)	90.00, 90.57, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	LEU	LEU	HIS	HIS	6	A	A	-5 - 0	17 - 22
2	1	1	LEU	LEU	HIS	HIS	6	B	B	-5 - 0	17 - 22
3	1	1	LEU	LEU	HIS	HIS	6	C	C	-5 - 0	17 - 22
4	1	1	LEU	LEU	HIS	HIS	6	D	D	-5 - 0	17 - 22
5	1	1	TYR	TYR	HIS	HIS	6	E	E	-4 - 0	18 - 22
6	1	1	LEU	LEU	HIS	HIS	6	F	F	-5 - 0	17 - 22
7	2	1	MET	MET	LEU	LEU	1	A	A	1 - 51	23 - 73
8	2	1	MET	MET	LEU	LEU	1	B	B	1 - 51	23 - 73
9	2	1	MET	MET	LEU	LEU	1	C	C	1 - 51	23 - 73
10	2	1	MET	MET	LEU	LEU	1	D	D	1 - 51	23 - 73
11	2	1	MET	MET	LEU	LEU	1	E	E	1 - 51	23 - 73
12	2	1	MET	MET	LEU	LEU	1	F	F	1 - 51	23 - 73
13	3	1	GLY	GLY	LEU	LEU	6	A	A	52 - 58	74 - 80
14	3	1	GLY	GLY	LEU	LEU	6	C	C	52 - 58	74 - 80
15	4	1	ARG	ARG	ALA	ALA	1	A	A	59 - 79	81 - 101
16	4	1	LEU	LEU	ALA	ALA	1	B	B	58 - 79	80 - 101
17	4	1	ARG	ARG	ALA	ALA	1	C	C	59 - 79	81 - 101
18	4	1	LEU	LEU	ALA	ALA	1	D	D	58 - 79	80 - 101
19	4	1	LEU	LEU	ALA	ALA	1	E	E	58 - 79	80 - 101
20	4	1	LEU	LEU	ALA	ALA	1	F	F	58 - 79	80 - 101
21	5	1	LEU	LEU	LEU	LEU	6	A	A	80 - 89	102 - 111
22	5	1	LEU	LEU	LEU	LEU	6	B	B	80 - 89	102 - 111
23	5	1	LEU	LEU	LEU	LEU	6	C	C	80 - 89	102 - 111
24	5	1	LEU	LEU	LEU	LEU	6	D	D	80 - 89	102 - 111
25	5	1	LEU	LEU	LEU	LEU	6	E	E	80 - 89	102 - 111
26	5	1	LEU	LEU	LEU	LEU	6	F	F	80 - 89	102 - 111
27	6	1	GLN	GLN	TYR	TYR	1	A	A	90 - 256	112 - 278
28	6	1	GLN	GLN	TYR	TYR	1	B	B	90 - 256	112 - 278
29	6	1	GLN	GLN	TYR	TYR	1	C	C	90 - 256	112 - 278
30	6	1	GLN	GLN	TYR	TYR	1	D	D	90 - 256	112 - 278
31	6	1	GLN	GLN	TYR	TYR	1	E	E	90 - 256	112 - 278
32	6	1	GLN	GLN	TYR	TYR	1	F	F	90 - 256	112 - 278
33	7	1	NAP	NAP	NAP	NAP	1	A	J	801
34	7	1	NAP	NAP	NAP	NAP	1	B	L	802
35	7	1	NAP	NAP	NAP	NAP	1	C	P	803
36	7	1	NAP	NAP	NAP	NAP	1	D	S	804
37	7	1	NAP	NAP	NAP	NAP	1	E	V	805
38	7	1	NAP	NAP	NAP	NAP	1	F	X	806
1	1	2	ASP	ASP	LYS	LYS	1	B	B	257 - 258	279 - 280
2	1	2	ASP	ASP	LYS	LYS	1	C	C	257 - 258	279 - 280
3	1	2	ASP	ASP	LYS	LYS	1	D	D	257 - 258	279 - 280
4	1	2	ASP	ASP	LYS	LYS	1	E	E	257 - 258	279 - 280
5	1	2	ASP	ASP	LYS	LYS	1	F	F	257 - 258	279 - 280

NCS ensembles :

ID
1
2

#1: Protein	Sepiapterin reductase / SPR Mass: 30550.080 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPR / Plasmid: SPRA-c005 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 References: UniProt: P35270, sepiapterin reductase (L-erythro-7,8-dihydrobiopterin-forming)
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 47.1 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG3350, lithium sulphate, BIS-TRIS, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.542 Å
Detector	Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 7, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.542 Å / Relative weight: 1
Reflection	Resolution: 2.5→62 Å / Num. obs: 52238 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2.5→2.64 Å / % possible all: 76.2

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MOSFLM		data reduction
CCP4	(SCALA)	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1SEP.pdb

1sep

Resolution: 2.5→47.1 Å / Cor.coef. F_o:F_c: 0.93 / Cor.coef. F_o:F_c free: 0.894 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24463	2622	5 %	RANDOM
R_work	0.20513	-	-	-
all	0.20707	49602	-	-
obs	0.20707	49602	89.42 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 28.298 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.19 Å²	0 Å²	-0.36 Å²
2-	-	-1.25 Å²	0 Å²
3-	-	-	1.43 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→47.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11571	0	304	241	12116

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	12068
X-RAY DIFFRACTION	r_angle_refined_deg	1.115	2.03	16433
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.064	5	1552
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.031	24.083	436
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.531	15	1961
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.857	15	80
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	1949
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	8836
X-RAY DIFFRACTION	r_nbd_refined	0.189	0.2	5085
X-RAY DIFFRACTION	r_nbtor_refined	0.3	0.2	8243
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	472
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.191	0.2	140
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.129	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	0.4	1.5	7943
X-RAY DIFFRACTION	r_mcangle_it	0.727	2	12301
X-RAY DIFFRACTION	r_scbond_it	1.21	3	4625
X-RAY DIFFRACTION	r_scangle_it	1.938	4.5	4132

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1760	tight positional	0.04	0.05
1	2	B	1760	tight positional	0.03	0.05
1	3	C	1760	tight positional	0.04	0.05
1	4	D	1760	tight positional	0.03	0.05
1	5	E	1760	tight positional	0.03	0.05
1	6	F	1760	tight positional	0.03	0.05
2	1	B	14	tight positional	0.02	0.05
2	2	C	14	tight positional	0.04	0.05
2	3	D	14	tight positional	0.03	0.05
2	4	E	14	tight positional	0.02	0.05
2	5	F	14	tight positional	0.03	0.05
1	1	A	113	loose positional	1.41	5
1	2	B	113	loose positional	0.7	5
1	3	C	113	loose positional	0.8	5
1	4	D	113	loose positional	0.76	5
1	5	E	113	loose positional	0.6	5
1	6	F	113	loose positional	0.98	5
1	1	A	1760	tight thermal	1.9	10
1	2	B	1760	tight thermal	1.76	10
1	3	C	1760	tight thermal	1.85	10
1	4	D	1760	tight thermal	1.5	10
1	5	E	1760	tight thermal	1.27	10
1	6	F	1760	tight thermal	1.25	10
2	1	B	14	tight thermal	1.8	10
2	2	C	14	tight thermal	2.52	10
2	3	D	14	tight thermal	0.4	10
2	4	E	14	tight thermal	0.58	10
2	5	F	14	tight thermal	1.32	10
1	1	A	113	loose thermal	2.73	10
1	2	B	113	loose thermal	2.64	10
1	3	C	113	loose thermal	5.1	10
1	4	D	113	loose thermal	3.72	10
1	5	E	113	loose thermal	2.13	10
1	6	F	113	loose thermal	3.79	10

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.318	166	-
R_work	0.282	3086	-
obs	-	-	76.55 %

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	1.7107	-0.5846	-0.0006	2.5929	0.4553	2.1909	-0.0252	-0.0821	-0.1718	0.2003	0.1033	0.0343	0.1013	-0.0136	-0.0781	-0.2875	0.0147	0.0005	-0.1814	0.0236	-0.2131	22.0818	21.5903	10.7625
2	2.0661	-0.4488	-0.082	3.8199	0.562	1.9686	-0.0641	-0.2652	0.0914	0.3701	0.1459	-0.0598	-0.208	0.0785	-0.0818	-0.1016	0.0663	-0.0047	-0.1639	-0.0168	-0.2679	18.1871	50.2061	24.7828
3	2.9285	-0.3157	1.0194	2.1082	0.1778	3.8253	-0.0986	0.0888	0.2056	-0.0779	-0.0995	-0.0677	-0.3147	0.0172	0.1981	-0.2621	0.0106	-0.0385	-0.2152	-0.0233	-0.2065	-3.5062	-6.9032	23.8841
4	2.2114	-0.0251	0.3028	2.5212	0.1395	4.3589	-0.0856	-0.4381	0.1953	0.4614	-0.0012	-0.0276	-0.2078	-0.1059	0.0868	-0.0276	0.0904	-0.0692	-0.0415	-0.1207	-0.1826	-0.1672	-6.7036	55.6877
5	2.782	0.6719	-0.7932	4.7403	-1.6542	3.2015	-0.0004	0.4092	0.3182	-0.6408	0.023	0.1402	0.1309	-0.2197	-0.0226	-0.0076	0.025	0.0097	0.0194	0.0599	-0.1103	38.4504	47.8369	56.5757
6	2.7557	1.0428	-0.3937	5.5949	-1.1316	3.3194	-0.0054	-0.0543	-0.464	-0.2539	-0.2501	-0.2208	0.5025	-0.035	0.2555	0.0178	-0.0339	0.0941	-0.0603	-0.0212	-0.0929	35.4926	21.3787	73.1324

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 258	23 - 280
2	X-RAY DIFFRACTION	1	A	S	801
3	X-RAY DIFFRACTION	2	B	B	1 - 258	23 - 280
4	X-RAY DIFFRACTION	2	B	T	802
5	X-RAY DIFFRACTION	3	C	C	1 - 258	23 - 280
6	X-RAY DIFFRACTION	3	C	U	803
7	X-RAY DIFFRACTION	4	D	D	1 - 258	23 - 280
8	X-RAY DIFFRACTION	4	D	V	804
9	X-RAY DIFFRACTION	5	E	E	1 - 258	23 - 280
10	X-RAY DIFFRACTION	5	E	W	805
11	X-RAY DIFFRACTION	6	F	F	1 - 258	23 - 280
12	X-RAY DIFFRACTION	6	F	X	806

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