1IS8

Crystal structure of rat GTPCHI/GFRP stimulatory complex plus Zn

PDB DOI: https://doi.org/10.2210/pdb1IS8/pdb

Classification: HYDROLASE/PROTEIN BINDING
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2001-11-18 Released: 2002-02-20
Deposition Author(s): Maita, N., Okada, K., Hatakeyama, K., Hakoshima, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.245
R-Value Work: 0.219

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the stimulatory complex of GTP cyclohydrolase I and its feedback regulatory protein GFRP.

Maita, N., Okada, K., Hatakeyama, K., Hakoshima, T.

(2002) Proc Natl Acad Sci U S A 99: 1212-1217

PubMed: 11818540 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.022646999
Primary Citation of Related Structures:
1IS7, 1IS8

PubMed Abstract:
In the presence of phenylalanine, GTP cyclohydrolase I feedback regulatory protein (GFRP) forms a stimulatory 360-kDa complex with GTP cyclohydrolase I (GTPCHI), which is the rate-limiting enzyme in the biosynthesis of tetrahydrobiopterin. The crystal structure of the stimulatory complex reveals that the GTPCHI decamer is sandwiched by two GFRP homopentamers. Each GFRP pentamer forms a symmetrical five-membered ring similar to beta-propeller. Five phenylalanine molecules are buried inside each interface between GFRP and GTPCHI, thus enhancing the binding of these proteins. The complex structure suggests that phenylalanine-induced GTPCHI x GFRP complex formation enhances GTPCHI activity by locking the enzyme in the active state.

Organizational Affiliation

Department of Molecular Biology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan.

Macromolecule Content

Total Structure Weight: 357.73 kDa
Atom Count: 22,511
Modelled Residue Count: 2,760
Deposited Residue Count: 3,140
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP Cyclohydrolase I	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	230	Rattus norvegicus	Mutation(s): 0 EC: 3.5.4.16
UniProt
Find proteins for P22288 (Rattus norvegicus) Explore P22288 Go to UniProtKB: P22288
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22288
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP Cyclohydrolase I Feedback Regulatory Protein	K, L, M, N, O K, L, M, N, O, P, Q, R, S, T	84	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P70552 (Rattus norvegicus) Explore P70552 Go to UniProtKB: P70552
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P70552
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PHE Query on PHE Download Ideal Coordinates CCD File SDF format, chain FA [auth K] SDF format, chain IA [auth M] SDF format, chain KA [auth N] SDF format, chain LA [auth N] SDF format, chain NA [auth O] SDF format, chain PA [auth P] SDF format, chain RA [auth Q] SDF format, chain TA [auth R] SDF format, chain VA [auth S] SDF format, chain XA [auth T] MOL2 format, chain FA [auth K] MOL2 format, chain IA [auth M] MOL2 format, chain KA [auth N] MOL2 format, chain LA [auth N] MOL2 format, chain NA [auth O] MOL2 format, chain PA [auth P] MOL2 format, chain RA [auth Q] MOL2 format, chain TA [auth R] MOL2 format, chain VA [auth S] MOL2 format, chain XA [auth T] mmCIF format, chain FA [auth K] mmCIF format, chain IA [auth M] mmCIF format, chain KA [auth N] mmCIF format, chain LA [auth N] mmCIF format, chain NA [auth O] mmCIF format, chain PA [auth P] mmCIF format, chain RA [auth Q] mmCIF format, chain TA [auth R] mmCIF format, chain VA [auth S] mmCIF format, chain XA [auth T]	FA [auth K] IA [auth M] KA [auth N] LA [auth N] NA [auth O] FA [auth K], IA [auth M], KA [auth N], LA [auth N], NA [auth O], PA [auth P], RA [auth Q], TA [auth R], VA [auth S], XA [auth T]	PHENYLALANINE C₉ H₁₁ N O₂ COLNVLDHVKWLRT-QMMMGPOBSA-N		Interactions Focus chain FA [auth K] Focus chain IA [auth M] Focus chain KA [auth N] Focus chain LA [auth N] Focus chain NA [auth O] Focus chain PA [auth P] Focus chain RA [auth Q] Focus chain TA [auth R] Focus chain VA [auth S] Focus chain XA [auth T] Interactions & Density Focus chain FA [auth K] Focus chain IA [auth M] Focus chain KA [auth N] Focus chain LA [auth N] Focus chain NA [auth O] Focus chain PA [auth P] Focus chain RA [auth Q] Focus chain TA [auth R] Focus chain VA [auth S] Focus chain XA [auth T]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth H] SDF format, chain CA [auth I] SDF format, chain DA [auth J] SDF format, chain U [auth A] SDF format, chain V [auth B] SDF format, chain W [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain U [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth F]	AA [auth G] BA [auth H] CA [auth I] DA [auth J] U [auth A] AA [auth G], BA [auth H], CA [auth I], DA [auth J], U [auth A], V [auth B], W [auth C], X [auth D], Y [auth E], Z [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Focus chain Z [auth F]
K Query on K Download Ideal Coordinates CCD File SDF format, chain EA [auth K] SDF format, chain GA [auth L] SDF format, chain HA [auth M] SDF format, chain JA [auth N] SDF format, chain MA [auth O] SDF format, chain OA [auth P] SDF format, chain QA [auth Q] SDF format, chain SA [auth R] SDF format, chain UA [auth S] SDF format, chain WA [auth T] MOL2 format, chain EA [auth K] MOL2 format, chain GA [auth L] MOL2 format, chain HA [auth M] MOL2 format, chain JA [auth N] MOL2 format, chain MA [auth O] MOL2 format, chain OA [auth P] MOL2 format, chain QA [auth Q] MOL2 format, chain SA [auth R] MOL2 format, chain UA [auth S] MOL2 format, chain WA [auth T] mmCIF format, chain EA [auth K] mmCIF format, chain GA [auth L] mmCIF format, chain HA [auth M] mmCIF format, chain JA [auth N] mmCIF format, chain MA [auth O] mmCIF format, chain OA [auth P] mmCIF format, chain QA [auth Q] mmCIF format, chain SA [auth R] mmCIF format, chain UA [auth S] mmCIF format, chain WA [auth T]	EA [auth K] GA [auth L] HA [auth M] JA [auth N] MA [auth O] EA [auth K], GA [auth L], HA [auth M], JA [auth N], MA [auth O], OA [auth P], QA [auth Q], SA [auth R], UA [auth S], WA [auth T]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain EA [auth K] Focus chain GA [auth L] Focus chain HA [auth M] Focus chain JA [auth N] Focus chain MA [auth O] Focus chain OA [auth P] Focus chain QA [auth Q] Focus chain SA [auth R] Focus chain UA [auth S] Focus chain WA [auth T] Interactions & Density Focus chain EA [auth K] Focus chain GA [auth L] Focus chain HA [auth M] Focus chain JA [auth N] Focus chain MA [auth O] Focus chain OA [auth P] Focus chain QA [auth Q] Focus chain SA [auth R] Focus chain UA [auth S] Focus chain WA [auth T]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.245
R-Value Work: 0.219
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.9	α = 90
b = 111.43	β = 97.32
c = 125.91	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2002-02-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-02-20
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations