1N4Q | pdb_00001n4q

Protein Geranylgeranyltransferase type-I Complexed with a GGPP Analog and a KKKSKTKCVIL Peptide

PDB DOI: https://doi.org/10.2210/pdb1N4Q/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: 2.40 Å
R-Value Free:
0.234 (Depositor), 0.228 (DCC)
R-Value Work:
0.214 (Depositor), 0.207 (DCC)
R-Value Observed:
0.214 (Depositor)

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: 530.71 kDa
Atom Count: 33,546
Modeled Residue Count: 3,990
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MGM Query on MGM Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain EA [auth H] SDF format, chain HA [auth J] SDF format, chain KA [auth L] SDF format, chain T [auth B] SDF format, chain X [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain EA [auth H] MOL2 format, chain HA [auth J] MOL2 format, chain KA [auth L] MOL2 format, chain T [auth B] MOL2 format, chain X [auth D] mmCIF format, chain AA [auth F] mmCIF format, chain EA [auth H] mmCIF format, chain HA [auth J] mmCIF format, chain KA [auth L] mmCIF format, chain T [auth B] mmCIF format, chain X [auth D]	AA [auth F] EA [auth H] HA [auth J] KA [auth L] T [auth B] AA [auth F], EA [auth H], HA [auth J], KA [auth L], T [auth B], X [auth D]	2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE C₁₉ H₃₇ N O₇ P₂ OEMBPHBKZPOPBN-NWLVNBMCSA-N		Interactions Focus chain AA [auth F] Focus chain EA [auth H] Focus chain HA [auth J] Focus chain KA [auth L] Focus chain T [auth B] Focus chain X [auth D] Interactions & Density Focus chain AA [auth F] Focus chain EA [auth H] Focus chain HA [auth J] Focus chain KA [auth L] Focus chain T [auth B] Focus chain X [auth D]
GER Query on GER Download Ideal Coordinates CCD File SDF format, chain LA [auth R] MOL2 format, chain LA [auth R] mmCIF format, chain LA [auth R]	LA [auth R]	GERAN-8-YL GERAN C₂₀ H₃₄ HSOYJGBJQAKCNA-CAIKYXSQSA-N		Interactions Focus chain LA [auth R] Interactions & Density Focus chain LA [auth R]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain CA [auth H] SDF format, chain FA [auth J] SDF format, chain JA [auth L] SDF format, chain S [auth B] SDF format, chain V [auth D] SDF format, chain Y [auth F] MOL2 format, chain CA [auth H] MOL2 format, chain FA [auth J] MOL2 format, chain JA [auth L] MOL2 format, chain S [auth B] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth F] mmCIF format, chain CA [auth H] mmCIF format, chain FA [auth J] mmCIF format, chain JA [auth L] mmCIF format, chain S [auth B] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth F]	CA [auth H] FA [auth J] JA [auth L] S [auth B] V [auth D] CA [auth H], FA [auth J], JA [auth L], S [auth B], V [auth D], Y [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth H] Focus chain FA [auth J] Focus chain JA [auth L] Focus chain S [auth B] Focus chain V [auth D] Focus chain Y [auth F] Interactions & Density Focus chain CA [auth H] Focus chain FA [auth J] Focus chain JA [auth L] Focus chain S [auth B] Focus chain V [auth D] Focus chain Y [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain DA [auth H] SDF format, chain GA [auth J] SDF format, chain IA [auth K] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain Z [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain GA [auth J] MOL2 format, chain IA [auth K] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain GA [auth J] mmCIF format, chain IA [auth K] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth F]	BA [auth G] DA [auth H] GA [auth J] IA [auth K] U [auth C] BA [auth G], DA [auth H], GA [auth J], IA [auth K], U [auth C], W [auth D], Z [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth G] Focus chain DA [auth H] Focus chain GA [auth J] Focus chain IA [auth K] Focus chain U [auth C] Focus chain W [auth D] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain DA [auth H] Focus chain GA [auth J] Focus chain IA [auth K] Focus chain U [auth C] Focus chain W [auth D] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.234 (Depositor), 0.228 (DCC)
R-Value Work: 0.214 (Depositor), 0.207 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 271.055	α = 90
b = 268.033	β = 131.73
c = 184.971	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: Version format compliance
Version 1.3: 2017-06-28
Changes: Advisory, Database references, Source and taxonomy, Structure summary
Version 1.4: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary