1N4R

Protein Geranylgeranyltransferase type-I Complexed with a Geranylgeranylated KKKSKTKCVIL Peptide Product

PDB DOI: https://doi.org/10.2210/pdb1N4R/pdb

Classification: TRANSFERASE
Organism(s): Rattus norvegicus, Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2002-11-01 Released: 2003-11-18
Deposition Author(s): Taylor, J.S., Reid, T.S., Casey, P.J., Beese, L.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.218
R-Value Work: 0.200
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure of mammalian protein geranylgeranyltransferase type-I

Taylor, J.S., Reid, T.S., Terry, K.L., Casey, P.J., Beese, L.S.

(2003) EMBO J 22: 5963-5974

PubMed: 14609943 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1093/emboj/cdg571
Primary Citation of Related Structures:
1N4P, 1N4Q, 1N4R, 1N4S

PubMed Abstract:
Protein geranylgeranyltransferase type-I (GGTase-I), one of two CaaX prenyltransferases, is an essential enzyme in eukaryotes. GGTase-I catalyzes C-terminal lipidation of >100 proteins, including many GTP- binding regulatory proteins. We present the first structural information for mammalian GGTase-I, including a series of substrate and product complexes that delineate the path of the chemical reaction. These structures reveal that all protein prenyltransferases share a common reaction mechanism and identify specific residues that play a dominant role in determining prenyl group specificity. This hypothesis was confirmed by converting farnesyltransferase (15-C prenyl substrate) into GGTase-I (20-C prenyl substrate) with a single point mutation. GGTase-I discriminates against farnesyl diphosphate (FPP) at the product turnover step through the inability of a 15-C FPP to displace the 20-C prenyl-peptide product. Understanding these key features of specificity is expected to contribute to optimization of anti-cancer and anti-parasite drugs.

Organizational Affiliation

Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.

Macromolecule Content

Total Structure Weight: 531.11 kDa
Atom Count: 33,129
Modelled Residue Count: 3,996
Deposited Residue Count: 4,590
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha	A, C, E, G, I A, C, E, G, I, K	377	Rattus norvegicus	Mutation(s): 0 Gene Names: Fnta EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (PDB Primary Data)
UniProt
Find proteins for Q04631 (Rattus norvegicus) Explore Q04631 Go to UniProtKB: Q04631
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04631
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl transferase type-1 subunit beta	B, D, F, H, J B, D, F, H, J, L	377	Rattus norvegicus	Mutation(s): 0 Gene Names: Pggt1b EC: 2.5.1.59
UniProt
Find proteins for P53610 (Rattus norvegicus) Explore P53610 Go to UniProtKB: P53610
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53610
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b	M, N, O, P, Q M, N, O, P, Q, R	11	Homo sapiens	Mutation(s): 0 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Explore P01116 Go to UniProtKB: P01116
PHAROS: P01116 GTEx: ENSG00000133703
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01116
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GER Query on GER Download Ideal Coordinates CCD File SDF format, chain RA [auth M] SDF format, chain SA [auth N] SDF format, chain TA [auth O] SDF format, chain UA [auth P] SDF format, chain VA [auth Q] SDF format, chain WA [auth R] MOL2 format, chain RA [auth M] MOL2 format, chain SA [auth N] MOL2 format, chain TA [auth O] MOL2 format, chain UA [auth P] MOL2 format, chain VA [auth Q] MOL2 format, chain WA [auth R] mmCIF format, chain RA [auth M] mmCIF format, chain SA [auth N] mmCIF format, chain TA [auth O] mmCIF format, chain UA [auth P] mmCIF format, chain VA [auth Q] mmCIF format, chain WA [auth R]	RA [auth M] SA [auth N] TA [auth O] UA [auth P] VA [auth Q] RA [auth M], SA [auth N], TA [auth O], UA [auth P], VA [auth Q], WA [auth R]	GERAN-8-YL GERAN C₂₀ H₃₄ HSOYJGBJQAKCNA-CAIKYXSQSA-N		Interactions Focus chain RA [auth M] Focus chain SA [auth N] Focus chain TA [auth O] Focus chain UA [auth P] Focus chain VA [auth Q] Focus chain WA [auth R]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain FA [auth G] SDF format, chain JA [auth I] SDF format, chain OA [auth K] SDF format, chain S [auth A] SDF format, chain W [auth C] MOL2 format, chain AA [auth E] MOL2 format, chain FA [auth G] MOL2 format, chain JA [auth I] MOL2 format, chain OA [auth K] MOL2 format, chain S [auth A] MOL2 format, chain W [auth C] mmCIF format, chain AA [auth E] mmCIF format, chain FA [auth G] mmCIF format, chain JA [auth I] mmCIF format, chain OA [auth K] mmCIF format, chain S [auth A] mmCIF format, chain W [auth C]	AA [auth E] FA [auth G] JA [auth I] OA [auth K] S [auth A] AA [auth E], FA [auth G], JA [auth I], OA [auth K], S [auth A], W [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain FA [auth G] Focus chain JA [auth I] Focus chain OA [auth K] Focus chain S [auth A] Focus chain W [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain IA [auth H] SDF format, chain MA [auth J] SDF format, chain QA [auth L] SDF format, chain U [auth B] SDF format, chain Z [auth D] MOL2 format, chain DA [auth F] MOL2 format, chain IA [auth H] MOL2 format, chain MA [auth J] MOL2 format, chain QA [auth L] MOL2 format, chain U [auth B] MOL2 format, chain Z [auth D] mmCIF format, chain DA [auth F] mmCIF format, chain IA [auth H] mmCIF format, chain MA [auth J] mmCIF format, chain QA [auth L] mmCIF format, chain U [auth B] mmCIF format, chain Z [auth D]	DA [auth F] IA [auth H] MA [auth J] QA [auth L] U [auth B] DA [auth F], IA [auth H], MA [auth J], QA [auth L], U [auth B], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth F] Focus chain IA [auth H] Focus chain MA [auth J] Focus chain QA [auth L] Focus chain U [auth B] Focus chain Z [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain GA [auth H] SDF format, chain KA [auth J] SDF format, chain PA [auth L] SDF format, chain T [auth B] SDF format, chain X [auth D] MOL2 format, chain BA [auth F] MOL2 format, chain GA [auth H] MOL2 format, chain KA [auth J] MOL2 format, chain PA [auth L] MOL2 format, chain T [auth B] MOL2 format, chain X [auth D] mmCIF format, chain BA [auth F] mmCIF format, chain GA [auth H] mmCIF format, chain KA [auth J] mmCIF format, chain PA [auth L] mmCIF format, chain T [auth B] mmCIF format, chain X [auth D]	BA [auth F] GA [auth H] KA [auth J] PA [auth L] T [auth B] BA [auth F], GA [auth H], KA [auth J], PA [auth L], T [auth B], X [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain GA [auth H] Focus chain KA [auth J] Focus chain PA [auth L] Focus chain T [auth B] Focus chain X [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain LA [auth J] SDF format, chain NA [auth K] SDF format, chain V [auth C] SDF format, chain Y [auth D] MOL2 format, chain CA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain LA [auth J] MOL2 format, chain NA [auth K] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain CA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain LA [auth J] mmCIF format, chain NA [auth K] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D]	CA [auth F] EA [auth G] HA [auth H] LA [auth J] NA [auth K] CA [auth F], EA [auth G], HA [auth H], LA [auth J], NA [auth K], V [auth C], Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain LA [auth J] Focus chain NA [auth K] Focus chain V [auth C] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.218
R-Value Work: 0.200
R-Value Observed: 0.200
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 272.068	α = 90
b = 268.801	β = 131.55
c = 185.31	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-11-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-11-18
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-06-28
Changes: Database references, Source and taxonomy, Structure summary
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary