PDBsum entry: 1lqb

Gene regulation

PDB id: 1lqb

Contents

Protein chains

104 a.a. *

88 a.a. *

150 a.a. *

18 a.a. *

Ligands

SO4

Waters ×84

* Residue conservation analysis

PDB id:

1lqb

Name:

Gene regulation

Title:

Crystal structure of a hydroxylated hif-1 alpha peptide bound to the pvhl/elongin-c/elongin-b complex

Structure:

Elongin b. Chain: a. Synonym: transcription elongation factor b, polypeptide 2. Engineered: yes. Elongin c. Chain: b. Fragment: residues 17-112. Synonym: transcription elongation factor b (siii), polypeptide 1.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: the peptide was synthesized with a biotin tag at the n-terminus and with p564 as a 4(r) hydroxyproline. The sequence of the peptide is naturally

Biol. unit:

Tetramer (from PQS)

Resolution:

2.00Å R-factor: 0.225 R-free: 0.277

Authors:

W.C.Hon,M.I.Wilson,K.Harlos,T.D.Claridge,C.J.Schofield, C.W.Pugh,P.H.Maxwell,P.J.Ratcliffe,D.I.Stuart,E.Y.Jones

Key ref:

W.C.Hon et al. (2002). Structural basis for the recognition of hydroxyproline in HIF-1 alpha by pVHL. Nature, 417, 975-978. PubMed id: 12050673 DOI: 10.1038/nature00767

Date:

09-May-02 Release date: 03-Jul-02

Protein chain

Q15370  (ELOB_HUMAN) -  Transcription elongation factor B polypeptide 2

Seq: 118 a.a.

Struc: 104 a.a.

Protein chain

Q15369  (ELOC_HUMAN) -  Transcription elongation factor B polypeptide 1

Seq: 112 a.a.

Struc: 88 a.a.

Protein chain

P40337  (VHL_HUMAN) -  Von Hippel-Lindau disease tumor suppressor

Seq: 213 a.a.

Struc: 150 a.a.

Protein chain

Q16665  (HIF1A_HUMAN) -  Hypoxia-inducible factor 1-alpha

Seq: 826 a.a.

Struc: 18 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (3 terms)
• Biological process: protein complex assembly (6 terms)
• Biochemical function: protein binding (1 term)

DOI no: 10.1038/nature00767

Nature 417:975-978 (2002)

PubMed id: 12050673

Structural basis for the recognition of hydroxyproline in HIF-1 alpha by pVHL.

W.C.Hon, M.I.Wilson, K.Harlos, T.D.Claridge, C.J.Schofield, C.W.Pugh, P.H.Maxwell, P.J.Ratcliffe, D.I.Stuart, E.Y.Jones.

ABSTRACT

Hypoxia-inducible factor-1 (HIF-1) is a transcriptional complex that controls cellular and systemic homeostatic responses to oxygen availability. HIF-1 alpha is the oxygen-regulated subunit of HIF-1, an alpha beta heterodimeric complex. HIF-1 alpha is stable in hypoxia, but in the presence of oxygen it is targeted for proteasomal degradation by the ubiquitination complex pVHL, the protein of the von Hippel Lindau (VHL) tumour suppressor gene and a component of an E3 ubiquitin ligase complex. Capture of HIF-1 alpha by pVHL is regulated by hydroxylation of specific prolyl residues in two functionally independent regions of HIF-1 alpha. The crystal structure of a hydroxylated HIF-1 alpha peptide bound to VCB (pVHL, elongins C and B) and solution binding assays reveal a single, conserved hydroxyproline-binding pocket in pVHL. Optimized hydrogen bonding to the buried hydroxyprolyl group confers precise discrimination between hydroxylated and unmodified prolyl residues. This mechanism provides a new focus for development of therapeutic agents to modulate cellular responses to hypoxia.

Selected figure(s)

Figure 2.
Figure 2: Structure of VCB -CODD complex, and sequence alignments of HIF ODD regions and pVHL. a, b, Surface rendering of the VCB -CODD complex with the secondary structures revealed underneath the semitransparent surface. Two regions seen in the current structure but not included in the previously reported model of apo VCB^15 are circled in elongin B (residues 99 -104) and pVHL (residues 205 -210). The C-terminal tail of elongin B makes newly observed contacts with the domain (V170 and N174) of pVHL. The still-unobserved region (residues 50 -57) in elongin C is modelled as a dotted loop. c, d, Sequence alignments of the CODD-binding region of pVHL domain (c) and of the ODD motifs of HIF homologues (d). Residues that form van der Waals (VDW) contacts are indicated by 'v'. 'w' denotes single hydrogen bonds (H-bonds) formed with a key water molecule (see Fig. 3d), as opposed to those formed between pVHL and CODD (see Fig. 3a, b). Arrows denote -strands. VHL disease missense mutations17 that occur in the CODD-binding region of pVHL are listed.

Figure 3.
Figure 3: CODD -pVHL interactions. a, b, Views of site 1 (a) and site 2 (b). CODD and CODD-contacting residues of pVHL are shown as stick models (colour scheme as in Fig. 1), whereas pVHL, elongin C and elongin B are rendered as van der Waals surfaces using the colour scheme of Fig. 2. Dotted lines represent electrostatic bonds. Residues for pVHL are labelled in white; those for CODD are in black. c, Views of the Hyp-binding pocket, illustrating its surface complementarity. The van der Waals surface of the ODD motif, LAHyp, is rendered solid and coloured by atom type (as in Fig. 1). The surface of pVHL is rendered as a mesh object with both the front and rear planes clipped away. Inset, side view of Hyp. d, The hydrogen-bonding network involved in binding of the Hyp564 hydroxyl group. The side chain of L562 (CODD) has been omitted for clarity. The red sphere in a, c and d represents a key water molecule. a has an approximately similar orientation to that of Fig. 2a, whereas the view in b is rotated from that in a by 70 degrees about the vertical axis.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2002, 417, 975-978) copyright 2002.

Figures were selected by the author.