PDBsum entry 3a44

Metal binding protein

PDB id: 3a44

Contents

Protein chains

137 a.a. *

122 a.a. *

127 a.a. *

Metals

_ZN ×4

* Residue conservation analysis

PDB id:

3a44

Name:

Metal binding protein

Title:

Crystal structure of hypa in the dimeric form

Structure:

Hydrogenase nickel incorporation protein hypa. Chain: a, b, c, d. Synonym: hypa. Engineered: yes

Source:

Pyrococcus kodakaraensis. Thermococcus kodakaraensis. Organism_taxid: 69014. Strain: kod1. Gene: hypa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.31Å R-factor: 0.292 R-free: 0.337

Authors:

S.Watanabe,T.Arai,R.Matsumi,H.Atomi,T.Imanaka,K.Miki

Key ref:

S.Watanabe et al. (2009). Crystal structure of HypA, a nickel-binding metallochaperone for [NiFe] hydrogenase maturation. J Mol Biol, 394, 448-459. PubMed id: 19769985 DOI: 10.1016/j.jmb.2009.09.030

Date:

30-Jun-09 Release date: 06-Oct-09

Protein chains

Q5JIH3  (HYPA_THEKO) -  Hydrogenase maturation factor HypA from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

Seq: 139 a.a.

Struc: 137 a.a.

Protein chain

Q5JIH3  (HYPA_THEKO) -  Hydrogenase maturation factor HypA from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

Seq: 139 a.a.

Struc: 122 a.a.

Protein chain

Q5JIH3  (HYPA_THEKO) -  Hydrogenase maturation factor HypA from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

Seq: 139 a.a.

Struc: 127 a.a.

DOI no: 10.1016/j.jmb.2009.09.030

J Mol Biol 394:448-459 (2009)

PubMed id: 19769985

Crystal structure of HypA, a nickel-binding metallochaperone for [NiFe] hydrogenase maturation.

S.Watanabe, T.Arai, R.Matsumi, H.Atomi, T.Imanaka, K.Miki.

ABSTRACT

HypA is one of the auxiliary proteins involved in the maturation of [NiFe] hydrogenases. By an unknown mechanism, HypA functions as a metallochaperone in the insertion of the Ni atom into hydrogenases. We have determined the crystal structures of HypA from Thermococcus kodakaraensis KOD1 in both monomeric and dimeric states. The structure of the HypA monomer consists of Ni- and Zn-binding domains. The relative arrangement of the two metal-binding domains has been shown to be associated with local conformations of the conserved Ni-binding motif, suggesting a communication between the Ni- and Zn-binding sites. The HypA dimer has been shown to be stabilized by unexpected domain swapping through archaea-specific linker helices. In addition, the hexameric structure of HypA is formed in the crystal packing. Several hydrogen bonds and hydrophobic interactions stabilize the hexamer interface. These findings suggest the functional diversity of HypA proteins.

Selected figure(s)

Figure 4.
Fig. 4. Domain flexibility of TkHypA. (a) A stereo view of the superposition of the main chain of the two HypA molecules in the asymmetric unit. The NiBD and ZnBD of mol A are colored in green and magenta, respectively, and those of mol B are in cyan and light pink, respectively. The insertion region is omitted for clarity. (b) An anomalous difference Fourier map around the zinc finger motif of mol B contoured at 7.5σ (red).

Figure 6.
Fig. 6. Domain swapped dimer of TkHypA. (a) A stereo view of the overall structure of the TkHypA dimer shown in a ribbon representation. The NiBD, insertion region, and ZnBD of a protomer are shown in the same colors as in Fig. 1a. The corresponding regions of the counterpart are presented in a light-colored model. (b) A topology diagram of the TkHypA dimer. (c) The protomer structure in the dimer. (d) A superposition of the two dimers in the asymmetric unit based on the NiBD of the protomer.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 394, 448-459) copyright 2009.

Figures were selected by an automated process.