PDBsum entry 4ogr

Transferase/viral protein

PDB id: 4ogr

Contents

Protein chains

315 a.a.

255 a.a.

55 a.a.

36 a.a.

54 a.a.

50 a.a.

Ligands

ADN ×3

Metals

_ZN ×6

Waters ×37

PDB id:

4ogr

Name:

Transferase/viral protein

Title:

Crystal structure of p-tefb complex with aff4 and tat

Structure:

Cyclin-dependent kinase 9. Chain: a, e, i. Fragment: unp residues 1-330. Synonym: c-2k, cell division cycle 2-like protein kinase 4, cell division protein kinase 9, serine/threonine-protein kinase pitalre, tat-associated kinase complex catalytic subunit. Engineered: yes. Cyclin-t1. Chain: b, f, k.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cdk9, cdc2l4, tak. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Gene: ccnt1. Gene: aff4, af5q31, mcef, hspc092. Expressed in: escherichia coli.

Resolution:

3.00Å R-factor: 0.206 R-free: 0.232

Authors:

U.Schulze-Gahmen,T.Alber

Key ref:

U.Schulze-Gahmen et al. (2014). AFF4 binding to Tat-P-TEFb indirectly stimulates TAR recognition of super elongation complexes at the HIV promoter. Elife, 3, e02375. PubMed id: 24843025

Date:

16-Jan-14 Release date: 07-May-14

Protein chains

P50750  (CDK9_HUMAN) -  Cyclin-dependent kinase 9 from Homo sapiens

Seq: 372 a.a.

Struc: 315 a.a.*

Protein chains

O60563  (CCNT1_HUMAN) -  Cyclin-T1 from Homo sapiens

Seq: 726 a.a.

Struc: 255 a.a.

Protein chain

Q9UHB7  (AFF4_HUMAN) -  AF4/FMR2 family member 4 from Homo sapiens

Seq: 1163 a.a.

Struc: 55 a.a.

Protein chain

Q9UHB7  (AFF4_HUMAN) -  AF4/FMR2 family member 4 from Homo sapiens

Seq: 1163 a.a.

Struc: 36 a.a.

Protein chain

Q9UHB7  (AFF4_HUMAN) -  AF4/FMR2 family member 4 from Homo sapiens

Seq: 1163 a.a.

Struc: 54 a.a.

Protein chains

P69698  (TAT_HV1H3) -  Protein Tat from Human immunodeficiency virus type 1 group M subtype B (isolate HXB3)

Seq: 86 a.a.

Struc: 49 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: Chains A, E, I: E.C.2.7.11.22 - cyclin-dependent kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] (Bound ligand (Het Group name = ADN) matches with 70.37% similarity) + ADP + H(+)

L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] (Bound ligand (Het Group name = ADN) matches with 70.37% similarity) + ADP + H(+)

• Enzyme class 3: Chains A, E, I: E.C.2.7.11.23 - [RNA-polymerase]-subunit kinase.
• Reaction: [DNA-directed RNA polymerase] + ATP = phospho-[DNA-directed RNA polymerase] + ADP + H⁺

[DNA-directed RNA polymerase] + ATP = phospho-[DNA-directed RNA polymerase] (Bound ligand (Het Group name = ADN) matches with 70.37% similarity) + ADP + 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

Elife 3:e02375 (2014)

PubMed id: 24843025

AFF4 binding to Tat-P-TEFb indirectly stimulates TAR recognition of super elongation complexes at the HIV promoter.

U.Schulze-Gahmen, H.Lu, Q.Zhou, T.Alber.

ABSTRACT

Superelongation complexes (SECs) are essential for transcription elongation of many human genes, including the integrated HIV-1 genome. At the HIV-1 promoter, the viral Tat protein binds simultaneously to the nascent TAR RNA and the CycT1 subunit of the P-TEFb kinase in a SEC. To understand the preferential recruitment of SECs by Tat and TAR, we determined the crystal structure of a quaternary complex containing Tat, P-TEFb, and the SEC scaffold, AFF4. Tat and AFF4 fold on the surface of CycT1 and interact directly. Interface mutations in the AFF4 homolog AFF1 reduced Tat-AFF1 affinity in vivo and Tat-dependent transcription from the HIV promoter. AFF4 binding in the presence of Tat partially orders the CycT1 Tat-TAR recognition motif and increases the affinity of Tat-P-TEFb for TAR 30-fold. These studies indicate that AFF4 acts as a two-step filter to increase the selectivity of Tat and TAR for SECs over P-TEFb alone.DOI: http://dx.doi.org/10.7554/eLife.02375.001.