PDBsum entry 1jm4

Transferase

PDB id: 1jm4

Contents

Protein chains

11 a.a.

118 a.a. *

* Residue conservation analysis

PDB id:

1jm4

Name:

Transferase

Title:

Nmr structure of p/caf bromodomain in complex with HIV-1 tat peptide

Structure:

HIV-1 tat peptide. Chain: a. Engineered: yes. P300/cbp-associated factor. Chain: b. Fragment: bromodomain. Synonym: p/caf. Engineered: yes

Source:

Synthetic: yes. Other_details: the peptide was chemically synthesized.. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

25 models

Authors:

S.Mujtaba,Y.He,L.Zeng,A.Farooq,J.E.Carlson,M.Ott,E.Verdin,M.-M.Zhou

Key ref:

S.Mujtaba et al. (2002). Structural basis of lysine-acetylated HIV-1 Tat recognition by PCAF bromodomain. Mol Cell, 9, 575-586. PubMed id: 11931765 DOI: 10.1016/S1097-2765(02)00483-5

Date:

17-Jul-01 Release date: 17-Jul-02

Protein chain

P04610  (TAT_HV1BR) -  Protein Tat from Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)

Seq: 86 a.a.

Struc: 11 a.a.*

Protein chain

Q92831  (KAT2B_HUMAN) -  Histone acetyltransferase KAT2B from Homo sapiens

Seq: 832 a.a.

Struc: 118 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chain B: E.C.2.3.1.48 - histone acetyltransferase.
• Reaction: L-lysyl-[protein] + acetyl-CoA = N₆-acetyl-L-lysyl-[protein] + CoA + H⁺
• Enzyme class 2: Chain B: E.C.2.3.1.57 - diamine N-acetyltransferase.
• Reaction: an alkane-alpha,omega-diamine + acetyl-CoA = an N-acetylalkane- alpha,omega-diamine + CoA + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/S1097-2765(02)00483-5

Mol Cell 9:575-586 (2002)

PubMed id: 11931765

Structural basis of lysine-acetylated HIV-1 Tat recognition by PCAF bromodomain.

S.Mujtaba, Y.He, L.Zeng, A.Farooq, J.E.Carlson, M.Ott, E.Verdin, M.M.Zhou.

ABSTRACT

The human immunodeficiency virus type 1 (HIV-1) trans-activator protein Tat stimulates transcription of the integrated HIV-1 genome and promotes viral replication in infected cells. Tat transactivation activity is dependent on lysine acetylation and its association with nuclear histone acetyltransferases p300/CBP (CREB binding protein) and p300/CBP-associated factor (PCAF). Here, we show that the bromodomain of PCAF binds specifically to HIV-1 Tat acetylated at lysine 50 and that this interaction competes effectively against HIV-1 TAR RNA binding to the lysine-acetylated Tat. The three-dimensional solution structure of the PCAF bromodomain in complex with a lysine 50-acetylated Tat peptide together with biochemical analyses provides the structural basis for the specificity of this molecular recognition and reveals insights into the differences in ligand selectivity of bromodomains.

Selected figure(s)

Figure 2.
Figure 2. NMR Structure of the PCAF Bromodomain/Tat AcK50 Peptide Complex(A) Stereoview of the backbone atoms (N, Cα, and C′) of 25 superimposed NMR-derived structures of the PCAF bromodomain (black) (showing residues 719–830) in complex with the Tat AcK50 peptide (green) (showing residues 46–55). Note that amino acid residues in the Tat peptide are described either according to their relative positions with respect to the acetyl-lysine in the sequence or for clarity numbered by their specific positions in the protein sequence of Tat.(B) Ribbons (Carson, 1991) representation of the average minimized NMR structure of the PCAF bromodomain/Tat peptide complex.(C) Stereoview of the Tat binding site in the bromodomain showing side chains of the protein (green) and peptide (blue) residues that are directly involved intermolecular interactions.(D) Stereoview of superimposition of the free (green) and ligand-bound (blue) structures of PCAF bromodomain showing side chain conformation of the residues in the Tat peptide binding site. The residues of the Tat peptide are colored in orange.(E) Surface representation of the Tat binding site of the bromodomain in ligand-bound (left) and free form (right). Protein residues important in ligand recognition are colored with the same color scheme in both structures. Residues indicated by an asterisk are almost completely buried in the free form structure.

Figure 4.
Figure 4. PCAF Bromodomain Competing against TAR RNA for Binding to Tat AcK50 Peptide(A) Superimposition of a selected region of 2D ^1H-^15N HSQC spectra of a ^13C/^15N-labeled PCAF bromodomain protein in the free form (black), in the presence of Tat AcK50 peptide (molar ratio of 1:1.2) (red), and in the presence of Tat AcK50 peptide and TAR RNA (molar ratio of 1:1.2:1 for protein:peptide:RNA) (blue). The spectra show chemical shift changes of the backbone amide resonances of protein residues due to peptide binding.(B) Superimposition of 2D ^1H-^13C HSQC spectra of the PCAF bromodomain collected under the same conditions as described in (A). The NMR spectra exhibit chemical shift changes of the side chain methyl group resonances of protein residues due to peptide binding. The same color-coding scheme was used as in (A). Arrows indicate chemical shift changes of protein NMR resonances from the free form (black) to the Tat AcK50 peptide-bound form (red). Note that only the bromodomain residues (i.e., A757 and V752) that directly interact with the Tat peptide, as shown in the three-dimensional structure, exhibited major chemical shift changes upon peptide binding or in competing against TAR RNA for binding to the Tat peptide. More importantly, addition of TAR RNA causes only small shifts of the protein signals from the Tat peptide-bound position toward the free form position, suggesting that the PCAF bromodomain competes effectively against TAR RNA for binding to the lysine-acetylated Tat peptide. We observed by NMR no significant nonspecific interactions between the protein and TAR RNA under these conditions.

The above figures are reprinted by permission from Cell Press: Mol Cell (2002, 9, 575-586) copyright 2002.

Figures were selected by an automated process.