1HZ7 - JenaLib

Theoretical Model (Jmol Viewer)

Title :   THE COMPLEX STRUCTURE OF FARNESYLTRANSFERASE BOUND WITH FARNESYL PYROPHOSPHATE, ZINC AND MAGNESIUM

Authors :   Y. -P. Pang, K. Xu, F. G. Prendergast

Date :   23 Jan 01 (Deposition) - 17 Jun 03 (Release) - 17 Jun 03 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A,B,_^#
( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Keywords :   Magnesium, Enzyme Catalysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. -P. Pang, K. Xu, F. G. Prendergast
Molecular Dynamics Simulation Of Farnesyltransferase Complexed With Co-Substrate Farnesyl Pyrophosphate: Insights Into Enzymatic Catalysis And Structure-Based Drug Design
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PROTEIN FARNESYLTRANSFERASE ALPHA SUBUNIT
	Chains	:	A
	EC Number	:	2.5.1.21
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Synonym	:	FTASE-ALPHA

Molecule 2 - PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT
	Chains	:	B
	EC Number	:	2.5.1.21
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Synonym	:	FTASE-BETA


Theoretical Model	:

( ^#: chains that contain no standard or modified protein/DNA/RNA residue)

Summary Information (see also Sequences/Alignments below)

Theoretical Model (3, 3)

No.	Name	Count	Type	Full Name
1	FPP	1	Ligand/Ion	FARNESYL DIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	ZN	1	Ligand/Ion	ZINC ION

(no "Site" information available for 1HZ7)

(no "SS Bond" information available for 1HZ7)

(no "Cis Peptide Bond" information available for 1HZ7)

(no "SAP(SNP)/Variant" information available for 1HZ7)

Theoretical Model (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PFTA	PS51147	Protein prenyltransferases alpha subunit repeat profile.	FNTA_RAT	112-146 147-181 215-249 182-214 255-289	3	- A:32-66 A:100-132 A:67-99 -

Theoretical Model (12, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000010588	1	ENSRNOE00000071243	chr6:99427967-99428155	189	FNTB_RAT	1-48	48	1	B:133-140	8
1.2	ENSRNOT00000010588	2	ENSRNOE00000071421	chr6:99447593-99447657	65	FNTB_RAT	49-70	22	1	B:141-162	22
1.3	ENSRNOT00000010588	3	ENSRNOE00000071602	chr6:99457445-99457517	73	FNTB_RAT	70-94	25	1	B:162-186	25
1.4	ENSRNOT00000010588	4	ENSRNOE00000071771	chr6:99459109-99459200	92	FNTB_RAT	95-125	31	1	B:187-217	31
1.5	ENSRNOT00000010588	5	ENSRNOE00000071976	chr6:99471356-99471502	147	FNTB_RAT	125-174	50	1	B:217-266	50
1.6	ENSRNOT00000010588	6	ENSRNOE00000072148	chr6:99471595-99471678	84	FNTB_RAT	174-202	29	1	B:266-294	29
1.7	ENSRNOT00000010588	7	ENSRNOE00000072321	chr6:99480586-99480672	87	FNTB_RAT	202-231	30	1	B:294-323	30
1.8	ENSRNOT00000010588	8	ENSRNOE00000072507	chr6:99489459-99489588	130	FNTB_RAT	231-274	44	1	B:323-366	44
1.9	ENSRNOT00000010588	9	ENSRNOE00000072695	chr6:99492633-99492765	133	FNTB_RAT	275-319	45	1	B:367-411	45
1.10	ENSRNOT00000010588	10	ENSRNOE00000072879	chr6:99504658-99504769	112	FNTB_RAT	319-356	38	1	B:411-448	38
1.11	ENSRNOT00000010588	11	ENSRNOE00000073070	chr6:99505820-99505934	115	FNTB_RAT	356-394	39	1	B:448-486	39
1.12	ENSRNOT00000010588	12	ENSRNOE00000238940	chr6:99510015-99511373	1359	FNTB_RAT	395-437	43	1	B:487-498	12

Theoretical Model

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:132
 aligned with FNTA_RAT | Q04631 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:132
                                   125       135       145       155       165       175       185       195       205       215       225       235       245  
             FNTA_RAT   116 AFKLTRDAIELNAANYTVWHFRRVLLRSLQKDLQEEMNYIIAIIEEQPKNYQVWHHRRVLVEWLKDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFRLWDNELQYVDQLLKEDVRNNSVWNQRHFVISNT 247
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE PFTA  PDB: - UniProt: 112-146  PFTA  PDB: A:32-66 UniProt: 147-181PFTA  PDB: A:67-99               PFTA  PDB: A:100-132              PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1hz7 A   1 AFKLTRDAIELNAANYTVWHFRRVLLRSLQKDLQEEMNYIIAIIEEQPKNYQVWHHRRVLVEWLKDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFRLWDNELQYVDQLLKEDVRNNSVWNQRHFVISNT 132
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:366
 aligned with FNTB_RAT | Q02293 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:366
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400      
             FNTB_RAT    41 ETVTSIEQAKVEEKIQEVFSSYKFNHLVPRLVLQREKHFHYLKRGLRQLTDAYECLDASRPWLCYWILHSLELLDEPIPQIVATDVCQFLELCQSPDGGFGGGPGQYPHLAPTYAAVNALCIIGTEEAYNVINREKLLQYLYSLKQPDGSFLMHVGGEVDVRSAYCAASVASLTNIITPDLFEGTAEWIARCQNWEGGIGGVPGMEAHGGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQHFGSGAMLHDVVMGVPENVLQPTHPVYNIGPD 406
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..............hhhhhhhhhhhhhhh....hhhhhhhhhhhhh................hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...................hhhhhh....hhhhhhhhh.............hhhhhhhhhhhhh......eeee..eeeehhhhhhhhhhhhhhheeee..eeee....hhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1Exon 1.2              ------------------------Exon 1.4  PDB: B:187-217       ------------------------------------------------Exon 1.6  PDB: B:266-294     ----------------------------Exon 1.8  PDB: B:323-366 UniProt: 231-274   --------------------------------------------Exon 1.10  PDB: B:411-448             --------------------------------------Exon 1.12    Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.3  PDB: B:162-186 ------------------------------Exon 1.5  PDB: B:217-266 UniProt: 125-174         ---------------------------Exon 1.7  PDB: B:294-323      -------------------------------------------Exon 1.9  PDB: B:367-411 UniProt: 275-319    ------------------------------------Exon 1.11  PDB: B:448-486              ------------ Transcript 1 (2)
                 1hz7 B 133 ETVTSIEQAKVEEKIQEVFSSYKFNHLVPRLVLQREKHFHYLKRGLRQLTDAYECLDASRPWLCYWILHSLELLDEPIPQIVATDVCQFLELCQSPDGGFGGGPGQYPHLAPTYAAVNALCIIGTEEAYNVINREKLLQYLYSLKQPDGSFLMHVGGEVDVRSAYCAASVASLTNIITPDLFEGTAEWIARCQNWEGGIGGVPGMEAHGGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQHFGSGAMLHDVVMGVPENVLQPTHPVYNIGPD 498
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 1HZ7)

(no "CATH Domain" information available for 1HZ7)

(no "Pfam Domain" information available for 1HZ7)

Theoretical Model(hide GO term definitions)

Chain A (FNTA_RAT | Q04631)

molecular function
	GO:0004662	CAAX-protein geranylgeranyltransferase activity	Catalysis of the reaction: geranylgeranyl diphosphate + protein-cysteine = S-geranylgeranyl-protein + diphosphate. This reaction is the formation of a thioether linkage between the C-1 atom of the geranylgeranyl group and a cysteine residue fourth from the C-terminus of the protein. The protein substrates have the C-terminal sequence CA1A2X, where the terminal residue, X, is preferably leucine and A2 should not be aromatic. Known substrates include most g-subunits of heterotrimeric G proteins and Ras-related GTPases such as members of the Ras and Rac/Rho families.
	GO:0008144	drug binding	Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	GO:0019840	isoprenoid binding	Interacting selectively and non-covalently with any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
	GO:0042277	peptide binding	Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
	GO:0004659	prenyltransferase activity	Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor).
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004660	protein farnesyltransferase activity	Catalysis of the reaction: farnesyl diphosphate + protein-cysteine = S-farnesyl protein + diphosphate.
	GO:0004661	protein geranylgeranyltransferase activity	Catalysis of the covalent addition of a geranylgeranyl (20-carbon isoprenoid) group via thioether linkages to a cysteine residue at or near the C terminus of a protein.
	GO:0008318	protein prenyltransferase activity	Catalysis of the covalent addition of an isoprenoid group such as a farnesyl or geranylgeranyl group via thioether linkages to a cysteine residue in a protein.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0051771	negative regulation of nitric-oxide synthase biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric-oxide synthase enzyme.
	GO:0045787	positive regulation of cell cycle	Any process that activates or increases the rate or extent of progression through the cell cycle.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0051770	positive regulation of nitric-oxide synthase biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme.
	GO:0018343	protein farnesylation	The covalent attachment of a farnesyl group to a protein.
	GO:0018344	protein geranylgeranylation	The covalent attachment of a geranylgeranyl group to a protein.
	GO:0018342	protein prenylation	The covalent attachment of a prenyl group to a protein; geranyl, farnesyl, or geranylgeranyl groups may be added.
	GO:0034097	response to cytokine	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
	GO:0010035	response to inorganic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inorganic substance stimulus.
	GO:0014070	response to organic cyclic compound	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
cellular component
	GO:0005953	CAAX-protein geranylgeranyltransferase complex	A heterodimeric enzyme, composed of an alpha and a beta subunit. Participates in the post-translational C-terminal modification of several small GTPases, allowing their targeting to the membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005965	protein farnesyltransferase complex	A protein complex that possesses protein farnesyltransferase activity.

Chain B (FNTB_RAT | Q02293)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0008144	drug binding	Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	GO:0004311	farnesyltranstransferase activity	Catalysis of the reaction: 2-trans,6-trans-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate.
	GO:0019840	isoprenoid binding	Interacting selectively and non-covalently with any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0042277	peptide binding	Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
	GO:0004659	prenyltransferase activity	Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor).
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004660	protein farnesyltransferase activity	Catalysis of the reaction: farnesyl diphosphate + protein-cysteine = S-farnesyl protein + diphosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0045787	positive regulation of cell cycle	Any process that activates or increases the rate or extent of progression through the cell cycle.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0048146	positive regulation of fibroblast proliferation	Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
	GO:0051770	positive regulation of nitric-oxide synthase biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme.
	GO:0018343	protein farnesylation	The covalent attachment of a farnesyl group to a protein.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0034097	response to cytokine	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
	GO:0010035	response to inorganic substance	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inorganic substance stimulus.
	GO:0014070	response to organic cyclic compound	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
	GO:0042060	wound healing	The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
	GO:0005875	microtubule associated complex	Any multimeric complex connected to a microtubule.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0005965	protein farnesyltransferase complex	A protein complex that possesses protein farnesyltransferase activity.

Theoretical Model
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(no "Sites" information available for 1hz7)

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(no "Cis Peptide Bonds" information available for 1hz7)

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(no "Related Entries Specified in the PDB File" available for 1HZ7)

Description

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Ligands, Modified Residues, Ions (3, 3)

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