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

Basic information

• Entry: Database: PDB / ID: 5ayz
• Title: CRYSTAL STRUCTURE OF HUMAN QUINOLINATE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH THE PRODUCT NICOTINATE MONONUCLEOTIDE
• 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 / cytosol / cytoplasm

Domain/homology:

Nicotinate-nucleotide pyrophosphorylase / Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-terminal domain / Quinolinate phosphoribosyl transferase, N-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:

NICOTINATE MONONUCLEOTIDE / Nicotinate-nucleotide pyrophosphorylase [carboxylating] / Nicotinate-nucleotide pyrophosphorylase [carboxylating]

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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: 4R3Y
Revision 1.0	Feb 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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]

J: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

K: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

L: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

hetero molecules

Summary:

• 387 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	387,022	24
Polymers	383,000	12
Non-polymers	4,022	12
Water	4,576	254

1

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]

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	193,511	12
Polymers	191,500	6
Non-polymers	2,011	6
Water	108	6

Symmetry operations:

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

Calculated values:

Buried area	26670 Å2
ΔGint	-170 kcal/mol
Surface area	58170 Å2
Method	PISA

2

G: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

H: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

I: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

J: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

K: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

L: Nicotinate-nucleotide pyrophosphorylase [carboxylating]

hetero molecules

Summary:

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

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	193,511	12
Polymers	191,500	6
Non-polymers	2,011	6
Water	108	6

Symmetry operations:

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

Calculated values:

Buried area	26740 Å2
ΔGint	-169 kcal/mol
Surface area	57750 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	109.186, 101.156, 151.643
Angle α, β, γ (deg.)	90.00, 92.49, 90.00
Int Tables number	4
Space group name H-M	P1211

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	A
2	9	J
1	10	A
2	10	K
1	11	A
2	11	L
1	12	B
2	12	C
1	13	B
2	13	D
1	14	B
2	14	E
1	15	B
2	15	F
1	16	B
2	16	G
1	17	B
2	17	H
1	18	B
2	18	I
1	19	B
2	19	J
1	20	B
2	20	K
1	21	B
2	21	L
1	22	C
2	22	D
1	23	C
2	23	E
1	24	C
2	24	F
1	25	C
2	25	G
1	26	C
2	26	H
1	27	C
2	27	I
1	28	C
2	28	J
1	29	C
2	29	K
1	30	C
2	30	L
1	31	D
2	31	E
1	32	D
2	32	F
1	33	D
2	33	G
1	34	D
2	34	H
1	35	D
2	35	I
1	36	D
2	36	J
1	37	D
2	37	K
1	38	D
2	38	L
1	39	E
2	39	F
1	40	E
2	40	G
1	41	E
2	41	H
1	42	E
2	42	I
1	43	E
2	43	J
1	44	E
2	44	K
1	45	E
2	45	L
1	46	F
2	46	G
1	47	F
2	47	H
1	48	F
2	48	I
1	49	F
2	49	J
1	50	F
2	50	K
1	51	F
2	51	L
1	52	G
2	52	H
1	53	G
2	53	I
1	54	G
2	54	J
1	55	G
2	55	K
1	56	G
2	56	L
1	57	H
2	57	I
1	58	H
2	58	J
1	59	H
2	59	K
1	60	H
2	60	L
1	61	I
2	61	J
1	62	I
2	62	K
1	63	I
2	63	L
1	64	J
2	64	K
1	65	J
2	65	L
1	66	K
2	66	L

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	A	A
2	9	J	J
1	10	A	A
2	10	K	K
1	11	A	A
2	11	L	L
1	12	B	B
2	12	C	C
1	13	B	B
2	13	D	D
1	14	B	B
2	14	E	E
1	15	B	B
2	15	F	F
1	16	B	B
2	16	G	G
1	17	B	B
2	17	H	H
1	18	B	B
2	18	I	I
1	19	B	B
2	19	J	J
1	20	B	B
2	20	K	K
1	21	B	B
2	21	L	L
1	22	C	C
2	22	D	D
1	23	C	C
2	23	E	E
1	24	C	C
2	24	F	F
1	25	C	C
2	25	G	G
1	26	C	C
2	26	H	H
1	27	C	C
2	27	I	I
1	28	C	C
2	28	J	J
1	29	C	C
2	29	K	K
1	30	C	C
2	30	L	L
1	31	D	D
2	31	E	E
1	32	D	D
2	32	F	F
1	33	D	D
2	33	G	G
1	34	D	D
2	34	H	H
1	35	D	D
2	35	I	I
1	36	D	D
2	36	J	J
1	37	D	D
2	37	K	K
1	38	D	D
2	38	L	L
1	39	E	E
2	39	F	F
1	40	E	E
2	40	G	G
1	41	E	E
2	41	H	H
1	42	E	E
2	42	I	I
1	43	E	E
2	43	J	J
1	44	E	E
2	44	K	K
1	45	E	E
2	45	L	L
1	46	F	F
2	46	G	G
1	47	F	F
2	47	H	H
1	48	F	F
2	48	I	I
1	49	F	F
2	49	J	J
1	50	F	F
2	50	K	K
1	51	F	F
2	51	L	L
1	52	G	G
2	52	H	H
1	53	G	G
2	53	I	I
1	54	G	G
2	54	J	J
1	55	G	G
2	55	K	K
1	56	G	G
2	56	L	L
1	57	H	H
2	57	I	I
1	58	H	H
2	58	J	J
1	59	H	H
2	59	K	K
1	60	H	H
2	60	L	L
1	61	I	I
2	61	J	J
1	62	I	I
2	62	K	K
1	63	I	I
2	63	L	L
1	64	J	J
2	64	K	K
1	65	J	J
2	65	L	L
1	66	K	K
2	66	L	L

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
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

Components

#1: Protein

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

Details:

Mass: 31916.645 Da / Num. of mol.: 12
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 J-401 K-401 L-401
ChemComp-NCN / NICOTINATE MONONUCLEOTIDE / NAMN

Details:

Mass: 335.204 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₁H₁₄NO₉P

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.18 ų/Da / Density % sol: 43.69 %
• Crystal grow: Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 ; Details: 10% PEG MME 2K, 0.01M POTASSIUM THIOCYANATE, PH 5.0, VAPOR DIFFUSION, TEMPERATURE 273.0K; PH range: 5

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: Dec 2, 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: 2.6→50 Å / Num. obs: 95727 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Net I/σ(I): 8.4
• Reflection shell: Resolution: 2.6→2.67 Å / % possible all: 94.1

Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	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: 2.6→44.14 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.952 / SU B: 10.927 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.256	5036	5 %	RANDOM
Rwork	0.226	-	-	-
obs	0.227	95727	99.2 %	-

• 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: 31.09 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.06 Å2	0 Å2	-0.05 Å2
2-	-	0.06 Å2	0 Å2
3-	-	-	0 Å2

Refinement step

Cycle: LAST / Resolution: 2.6→44.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25296	0	264	254	25814

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	26088
X-RAY DIFFRACTION	r_bond_other_d	0.01	0.02	25344
X-RAY DIFFRACTION	r_angle_refined_deg	2.05	1.983	35580
X-RAY DIFFRACTION	r_angle_other_deg	1.792	3	58212
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.394	5	3456
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.423	24.177	948
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.097	15	3924
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.261	15	132
X-RAY DIFFRACTION	r_chiral_restr	0.133	0.2	4164
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.021	29808
X-RAY DIFFRACTION	r_gen_planes_other	0.01	0.02	5604
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	16608	0.06
1	2	B	16608	0.06
2	1	A	16418	0.07
2	2	C	16418	0.07
3	1	A	16434	0.06
3	2	D	16434	0.06
4	1	A	16545	0.06
4	2	E	16545	0.06
5	1	A	16401	0.08
5	2	F	16401	0.08
6	1	A	16846	0.05
6	2	G	16846	0.05
7	1	A	16527	0.07
7	2	H	16527	0.07
8	1	A	16470	0.07
8	2	I	16470	0.07
9	1	A	16399	0.07
9	2	J	16399	0.07
10	1	A	16409	0.07
10	2	K	16409	0.07
11	1	A	16341	0.08
11	2	L	16341	0.08
12	1	B	16486	0.07
12	2	C	16486	0.07
13	1	B	16499	0.06
13	2	D	16499	0.06
14	1	B	16601	0.06
14	2	E	16601	0.06
15	1	B	16445	0.07
15	2	F	16445	0.07
16	1	B	16579	0.06
16	2	G	16579	0.06
17	1	B	16948	0.04
17	2	H	16948	0.04
18	1	B	16485	0.06
18	2	I	16485	0.06
19	1	B	16483	0.06
19	2	J	16483	0.06
20	1	B	16550	0.07
20	2	K	16550	0.07
21	1	B	16468	0.07
21	2	L	16468	0.07
22	1	C	16432	0.06
22	2	D	16432	0.06
23	1	C	16680	0.06
23	2	E	16680	0.06
24	1	C	16487	0.07
24	2	F	16487	0.07
25	1	C	16449	0.07
25	2	G	16449	0.07
26	1	C	16435	0.07
26	2	H	16435	0.07
27	1	C	16996	0.04
27	2	I	16996	0.04
28	1	C	16446	0.07
28	2	J	16446	0.07
29	1	C	16519	0.06
29	2	K	16519	0.06
30	1	C	16499	0.07
30	2	L	16499	0.07
31	1	D	16621	0.05
31	2	E	16621	0.05
32	1	D	16453	0.06
32	2	F	16453	0.06
33	1	D	16329	0.06
33	2	G	16329	0.06
34	1	D	16432	0.06
34	2	H	16432	0.06
35	1	D	16439	0.06
35	2	I	16439	0.06
36	1	D	16910	0.03
36	2	J	16910	0.03
37	1	D	16525	0.06
37	2	K	16525	0.06
38	1	D	16363	0.07
38	2	L	16363	0.07
39	1	E	16634	0.06
39	2	F	16634	0.06
40	1	E	16561	0.06
40	2	G	16561	0.06
41	1	E	16539	0.07
41	2	H	16539	0.07
42	1	E	16691	0.06
42	2	I	16691	0.06
43	1	E	16639	0.05
43	2	J	16639	0.05
44	1	E	16805	0.04
44	2	K	16805	0.04
45	1	E	16582	0.06
45	2	L	16582	0.06
46	1	F	16481	0.07
46	2	G	16481	0.07
47	1	F	16526	0.07
47	2	H	16526	0.07
48	1	F	16557	0.07
48	2	I	16557	0.07
49	1	F	16442	0.06
49	2	J	16442	0.06
50	1	F	16485	0.07
50	2	K	16485	0.07
51	1	F	16934	0.05
51	2	L	16934	0.05
52	1	G	16655	0.06
52	2	H	16655	0.06
53	1	G	16477	0.06
53	2	I	16477	0.06
54	1	G	16370	0.06
54	2	J	16370	0.06
55	1	G	16482	0.06
55	2	K	16482	0.06
56	1	G	16424	0.07
56	2	L	16424	0.07
57	1	H	16407	0.07
57	2	I	16407	0.07
58	1	H	16359	0.07
58	2	J	16359	0.07
59	1	H	16438	0.07
59	2	K	16438	0.07
60	1	H	16422	0.08
60	2	L	16422	0.08
61	1	I	16479	0.06
61	2	J	16479	0.06
62	1	I	16561	0.06
62	2	K	16561	0.06
63	1	I	16499	0.07
63	2	L	16499	0.07
64	1	J	16563	0.06
64	2	K	16563	0.06
65	1	J	16454	0.06
65	2	L	16454	0.06
66	1	K	16534	0.07
66	2	L	16534	0.07

LS refinement shell

Resolution: 2.6→2.67 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.418	380	-
Rwork	0.347	6619	-
obs	-	-	94.06 %