PDBsum entry 2bdh

Hydrolase

PDB id: 2bdh

Contents

Protein chain

223 a.a. *

Ligands

PBZ ×4

Metals

_ZN

Waters ×111

* Residue conservation analysis

PDB id:

2bdh

Name:

Hydrolase

Title:

Human kallikrein 4 complex with zinc and p-aminobenzamidine

Structure:

Kallikrein-4. Chain: a, b, c, d. Fragment: human kallikrein 4. Synonym: prostase, kallikrein-like protein 1, klk-l1, enamel matrix serine proteinase 1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: klk4, emsp1, prss17, psts. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

3.00Å R-factor: 0.233 R-free: 0.292

Authors:

M.Debela,W.Bode,P.Goettig,Structural Proteomics In Europe (Spine)

Key ref:

M.Debela et al. (2006). Crystal structures of human tissue kallikrein 4: activity modulation by a specific zinc binding site. J Mol Biol, 362, 1094-1107. PubMed id: 16950394 DOI: 10.1016/j.jmb.2006.08.003

Date:

20-Oct-05 Release date: 03-Oct-06

Protein chains

Q9Y5K2  (KLK4_HUMAN) -  Kallikrein-4 from Homo sapiens

Seq: 254 a.a.

Struc: 223 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.4.21.- - ?????

DOI no: 10.1016/j.jmb.2006.08.003

J Mol Biol 362:1094-1107 (2006)

PubMed id: 16950394

Crystal structures of human tissue kallikrein 4: activity modulation by a specific zinc binding site.

M.Debela, V.Magdolen, V.Grimminger, C.Sommerhoff, A.Messerschmidt, R.Huber, R.Friedrich, W.Bode, P.Goettig.

ABSTRACT

Human tissue kallikrein 4 (hK4) belongs to a 15-member family of closely related serine proteinases. hK4 is predominantly expressed in prostate, activates hK3/PSA, and is up-regulated in prostate and ovarian cancer. We have identified active monomers of recombinant hK4 besides inactive oligomers in solution. hK4 crystallised in the presence of zinc, nickel, and cobalt ions in three crystal forms containing cyclic tetramers and octamers. These structures display a novel metal site between His25 and Glu77 that links the 70-80 loop with the N-terminal segment. Micromolar zinc as present in prostatic fluid inhibits the enzymatic activity of hK4 against fluorogenic substrates. In our measurements, wild-type hK4 exhibited a zinc inhibition constant (IC50) of 16 microM including a permanent residual activity, in contrast to the zinc-independent mutants H25A and E77A. Since the Ile16 N terminus of wild-type hK4 becomes more accessible for acetylating agents in the presence of zinc, we propose that zinc affects the hK4 active site via the salt-bridge formed between the N terminus and Asp194 required for a functional active site. hK4 possesses an unusual 99-loop that creates a groove-like acidic S2 subsite. These findings explain the observed specificity of hK4 for the P1 to P4 substrate residues. Moreover, hK4 shows a negatively charged surface patch, which may represent an exosite for prime-side substrate recognition.

Selected figure(s)

Figure 3.
Figure 3. (a) Stereo view of the oligomeric architecture in the P4[1]2[1]2 hK4-Zn form. One hK4 tetramer is located in the asymmetric unit, highlighted by a transparent surface. This arrangement is pseudo-symmetrical, in contrast to the symmetrical tetramers of the P4 form. Only one zinc ion is bound per tetramer, displayed as a pink ball with electron density representing an anomalous Fourier map contoured at 3σ. Molecules that are symmetry-related by a crystallographic 2-fold axis are depicted in the same color. Both tetramers sit back to back and contact each other with a flat interaction surface resulting in an octameric assembly. (b) Top view of the octamer from the P4[1]2[1]2 crystals rotated by 90° with respect to (a). (c) Stereo representation of the asymmetric unit in the hK4-Co P2[1] crystal form, which contains two hk4 octamers. One cobalt ion is bound per pseudo-symmetrical tetramer, indicated by an anomalous Fourier map.

Figure 6.
Figure 6. Stereo view of the Ni^2+-binding site in the 70–80 loop of hK4, superimposed by the equivalent segments of hK1 in grey. The Ni^2+ is shown as a cyan ball, bound by four water molecules, Glu77 O^ε, and His25 N^ε2. The Ni^2+ ligand contacts are depicted as dotted lines. The electron density accounting for the coordinating water molecules is contoured at 1.0σ and that around nickel at 5.0σ. The most significant difference between the compared loops is one helical turn in hK4.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 362, 1094-1107) copyright 2006.

Figures were selected by an automated process.