PDB-5ayy: CRYSTAL STRUCTURE OF HUMAN QUINOLINATE PHOSPHORIBOSYLTRANSFERASE ...

Basic information

• Entry: Database: PDB / ID: 5ayy
• Title: CRYSTAL STRUCTURE OF HUMAN QUINOLINATE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH THE REACTANT QUINOLINATE
• Components: Nicotinate-nucleotide pyrophosphorylase [carboxylating]
• Keywords: TRANSFERASE

Function / homology

Function:

quinolinate catabolic process / nicotinate-nucleotide diphosphorylase (carboxylating) / nicotinate-nucleotide diphosphorylase (carboxylating) activity / Nicotinate metabolism / NAD metabolic process / NAD biosynthetic process / catalytic complex / extracellular exosome / identical protein binding / cytoplasm / cytosol

Domain/homology:

Nicotinate-nucleotide pyrophosphorylase / Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD / Quinolinate phosphoribosyl transferase, N-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-terminal domain / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldehyde Oxidoreductase; domain 3 / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Alpha Beta

Component:

QUINOLINIC ACID / Nicotinate-nucleotide pyrophosphorylase [carboxylating] / Nicotinate-nucleotide pyrophosphorylase [carboxylating]

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
• Authors: Youn, H.S. / Kim, T.G. / Kim, M.K. / Kang, G.B. / Kang, J.Y. / Seo, Y.J. / Lee, J.G. / An, J.Y. / Park, K.R. / Lee, Y. / Im, Y.J. / Lee, J.H. / Fukuoka, S.I. / Eom, S.H.
• Citation: Journal: Sci Rep / Year: 2016; Title: Structural Insights into the Quaternary Catalytic Mechanism of Hexameric Human Quinolinate Phosphoribosyltransferase, a Key Enzyme in de novo NAD Biosynthesis; Authors: Youn, H.S. / Kim, T.G. / Kim, M.K. / Kang, G.B. / Kang, J.Y. / Lee, J.G. / An, J.Y. / Park, K.R. / Lee, Y. / Im, Y.J. / Lee, J.H. / Eom, S.H.

History

Deposition	Sep 14, 2015	Deposition site: PDBJ / Processing site: PDBJ
Supersession	Feb 3, 2016	ID: 4R3X
Revision 1.0	Feb 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 29, 2020	Group: Derived calculations / Structure summary / Category: audit_author / pdbx_struct_oper_list Item: _audit_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _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.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Assembly

Deposited unit

A: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

B: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

C: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

D: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

E: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

F: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

G: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

H: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

I: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

hetero molecules

Summary:

• 289 kDa, 9 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	288,754	18
Polymers	287,250	9
Non-polymers	1,504	9
Water	667	37

1

A: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

C: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

D: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

G: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

H: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

I: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

hetero molecules

Summary:

• defined by author&software
• 193 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	192,503	12
Polymers	191,500	6
Non-polymers	1,003	6
Water	108	6

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	27450 Å2
ΔGint	-173 kcal/mol
Surface area	57730 Å2
Method	PISA

2

B: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

E: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

F: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

hetero molecules

B: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

E: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

F: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

hetero molecules

Summary:

• defined by author&software
• 193 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	192,503	12
Polymers	191,500	6
Non-polymers	1,003	6
Water	108	6

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	4_555	y,x,-z	1

Calculated values:

Buried area	27820 Å2
ΔGint	-169 kcal/mol
Surface area	57150 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	174.245, 174.245, 211.684
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3221

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	B
2	9	C
1	10	B
2	10	D
1	11	B
2	11	E
1	12	B
2	12	F
1	13	B
2	13	G
1	14	B
2	14	H
1	15	B
2	15	I
1	16	C
2	16	D
1	17	C
2	17	E
1	18	C
2	18	F
1	19	C
2	19	G
1	20	C
2	20	H
1	21	C
2	21	I
1	22	D
2	22	E
1	23	D
2	23	F
1	24	D
2	24	G
1	25	D
2	25	H
1	26	D
2	26	I
1	27	E
2	27	F
1	28	E
2	28	G
1	29	E
2	29	H
1	30	E
2	30	I
1	31	F
2	31	G
1	32	F
2	32	H
1	33	F
2	33	I
1	34	G
2	34	H
1	35	G
2	35	I
1	36	H
2	36	I

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 1 - 289 / Label seq-ID: 1 - 289

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	A	A
2	4	E	E
1	5	A	A
2	5	F	F
1	6	A	A
2	6	G	G
1	7	A	A
2	7	H	H
1	8	A	A
2	8	I	I
1	9	B	B
2	9	C	C
1	10	B	B
2	10	D	D
1	11	B	B
2	11	E	E
1	12	B	B
2	12	F	F
1	13	B	B
2	13	G	G
1	14	B	B
2	14	H	H
1	15	B	B
2	15	I	I
1	16	C	C
2	16	D	D
1	17	C	C
2	17	E	E
1	18	C	C
2	18	F	F
1	19	C	C
2	19	G	G
1	20	C	C
2	20	H	H
1	21	C	C
2	21	I	I
1	22	D	D
2	22	E	E
1	23	D	D
2	23	F	F
1	24	D	D
2	24	G	G
1	25	D	D
2	25	H	H
1	26	D	D
2	26	I	I
1	27	E	E
2	27	F	F
1	28	E	E
2	28	G	G
1	29	E	E
2	29	H	H
1	30	E	E
2	30	I	I
1	31	F	F
2	31	G	G
1	32	F	F
2	32	H	H
1	33	F	F
2	33	I	I
1	34	G	G
2	34	H	H
1	35	G	G
2	35	I	I
1	36	H	H
2	36	I	I

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36

Components

#1: Protein

A B C D E F G H I
Nicotinate-nucleotide pyrophosphorylase [carboxylating] / Quinolinate phosphoribosyltransferase [decarboxylating]

Details:

Mass: 31916.645 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HEL-S-90n, QPRT / Production host: Escherichia coli (E. coli)
References: UniProt: V9HWJ5, UniProt: Q15274*PLUS, nicotinate-nucleotide diphosphorylase (carboxylating)

#2: Chemical

A-401 B-401 C-401 D-401 E-401 F-401 G-401 H-401 I-401
ChemComp-NTM / QUINOLINIC ACID

Details:

Mass: 167.119 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₇H₅NO₄

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 3.23 ų/Da / Density % sol: 61.91 %
• Crystal grow: Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 ; Details: 8% PEG8000, 0.1M MEGNESIUM ACETATE, PH 8.0, VAPOR DIFFUSION, TEMPERATURE 273.0K; PH range: 8

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
• Detector: Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2013
• Radiation: Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9795 Å / Relative weight: 1
• Reflection: Resolution: 3.09→50 Å / Num. obs: 67428 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Net I/σ(I): 10.9
• Reflection shell: Resolution: 3.09→3.17 Å / % possible all: 96.2

Processing

Software

Name	Version	Classification
REFMAC	6.5.0	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LAR

3lar
PDB Unreleased entry

Resolution: 3.09→45.43 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.919 / SU B: 16.792 / SU ML: 0.284 / Cross valid method: THROUGHOUT / ESU R Free: 0.388 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.239	3421	5.1 %	RANDOM
Rwork	0.185	-	-	-
obs	0.229	60586	98.8 %	-

• 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: 56.38 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0 Å2	0 Å2	0 Å2
2-	-	0 Å2	0 Å2
3-	-	-	0 Å2

Refinement step

Cycle: LAST / Resolution: 3.09→45.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18972	0	108	37	19117

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	19420
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	18940
X-RAY DIFFRACTION	r_angle_refined_deg	1.747	1.974	26452
X-RAY DIFFRACTION	r_angle_other_deg	1.459	3	43471
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.575	5	2592
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.861	24.177	711
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.041	15	2943
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.636	15	99
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	3087
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	22326
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	4189
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	15963	0.09
1	2	B	15963	0.09
2	1	A	16806	0.06
2	2	C	16806	0.06
3	1	A	16763	0.06
3	2	D	16763	0.06
4	1	A	16822	0.05
4	2	E	16822	0.05
5	1	A	16705	0.06
5	2	F	16705	0.06
6	1	A	16695	0.06
6	2	G	16695	0.06
7	1	A	16645	0.06
7	2	H	16645	0.06
8	1	A	16811	0.06
8	2	I	16811	0.06
9	1	B	16015	0.09
9	2	C	16015	0.09
10	1	B	16011	0.09
10	2	D	16011	0.09
11	1	B	16007	0.09
11	2	E	16007	0.09
12	1	B	16013	0.09
12	2	F	16013	0.09
13	1	B	16057	0.09
13	2	G	16057	0.09
14	1	B	15945	0.09
14	2	H	15945	0.09
15	1	B	16018	0.09
15	2	I	16018	0.09
16	1	C	16737	0.05
16	2	D	16737	0.05
17	1	C	16849	0.05
17	2	E	16849	0.05
18	1	C	16828	0.05
18	2	F	16828	0.05
19	1	C	16826	0.05
19	2	G	16826	0.05
20	1	C	16786	0.05
20	2	H	16786	0.05
21	1	C	16962	0.04
21	2	I	16962	0.04
22	1	D	16743	0.06
22	2	E	16743	0.06
23	1	D	16775	0.06
23	2	F	16775	0.06
24	1	D	16882	0.05
24	2	G	16882	0.05
25	1	D	16764	0.06
25	2	H	16764	0.06
26	1	D	16821	0.05
26	2	I	16821	0.05
27	1	E	16857	0.05
27	2	F	16857	0.05
28	1	E	16951	0.04
28	2	G	16951	0.04
29	1	E	16717	0.06
29	2	H	16717	0.06
30	1	E	16993	0.04
30	2	I	16993	0.04
31	1	F	16919	0.06
31	2	G	16919	0.06
32	1	F	16812	0.06
32	2	H	16812	0.06
33	1	F	16895	0.05
33	2	I	16895	0.05
34	1	G	16872	0.05
34	2	H	16872	0.05
35	1	G	16954	0.04
35	2	I	16954	0.04
36	1	H	16826	0.05
36	2	I	16826	0.05

LS refinement shell

Resolution: 3.09→3.17 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.305	232	-
Rwork	0.292	4556	-
obs	-	-	96.18 %