PDBsum entry 4imy

Transferase

PDB id: 4imy

Contents

Protein chains

315 a.a.

250 a.a.

33 a.a.

53 a.a.

Ligands

AMP ×3

Waters ×19

PDB id:

4imy

Name:

Transferase

Title:

The aff4 scaffold binds human p-tefb adjacent to HIV tat

Structure:

Cyclin-dependent kinase 9. Chain: a, c, e. Fragment: 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, d, f.

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:

2.94Å R-factor: 0.209 R-free: 0.245

Authors:

T.Alber,U.Schulze-Gahmen

Key ref:

U.Schulze-Gahmen et al. (2013). The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat. Elife, 2, e00327. PubMed id: 23471103 DOI: 10.7554/eLife.00327

Date:

03-Jan-13 Release date: 13-Mar-13

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: 250 a.a.

Protein chains

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

Seq: 1163 a.a.

Struc: 33 a.a.

Protein chain

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

Seq: 1163 a.a.

Struc: 53 a.a.

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

Enzyme reactions

• Enzyme class 2: Chains A, C, E: 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 = AMP) matches with 85.19% similarity) + ADP + H(+)

L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] (Bound ligand (Het Group name = AMP) matches with 85.19% similarity) + ADP + H(+)

• Enzyme class 3: Chains A, C, E: 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 = AMP) matches with 85.19% 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

DOI no: 10.7554/eLife.00327

Elife 2:e00327 (2013)

PubMed id: 23471103

The AFF4 scaffold binds human P-TEFb adjacent to HIV Tat.

U.Schulze-Gahmen, H.Upton, A.Birnberg, K.Bao, S.Chou, N.J.Krogan, Q.Zhou, T.Alber.

ABSTRACT

No abstract given.