PDBsum entry 5dsl

Lyase

PDB id: 5dsl

Contents

Protein chain

257 a.a.

Ligands

GOL

Metals

_ZN

Waters ×403

PDB id:

5dsl

Name:

Lyase

Title:

Structure of co2 released holo-form of human carbonic anhydrase ii with 10 min warming

Structure:

Carbonic anhydrase 2. Chain: a. Synonym: carbonate dehydratase ii,carbonic anhydrasE C,cac,carbonic anhydrase ii,ca-ii. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ca2. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.45Å R-factor: 0.104 R-free: 0.147

Authors:

C.U.Kim,S.Y.Park,R.Mckenna

Key ref:

C.U.Kim et al. (2016). Tracking solvent and protein movement during CO2 release in carbonic anhydrase II crystals. Proc Natl Acad Sci U S A, 113, 5257-5262. PubMed id: 27114542

Date:

17-Sep-15 Release date: 04-May-16

Protein chain

P00918  (CAH2_HUMAN) -  Carbonic anhydrase 2 from Homo sapiens

Seq: 260 a.a.

Struc: 257 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.1.1 - carbonic anhydrase.
• Reaction: hydrogencarbonate + H⁺ = CO2 + H2O
• Cofactor: Zn(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

Proc Natl Acad Sci U S A 113:5257-5262 (2016)

PubMed id: 27114542

Tracking solvent and protein movement during CO2 release in carbonic anhydrase II crystals.

C.U.Kim, H.Song, B.S.Avvaru, S.M.Gruner, S.Park, R.McKenna.

ABSTRACT

Carbonic anhydrases are mostly zinc metalloenzymes that catalyze the reversible hydration/dehydration of CO2/HCO3 (-) Previously, the X-ray crystal structures of CO2-bound holo (zinc-bound) and apo (zinc-free) human carbonic anhydrase IIs (hCA IIs) were captured at high resolution. Here, we present sequential timeframe structures of holo- [T = 0 s (CO2-bound), 50 s, 3 min, 10 min, 25 min, and 1 h] and apo-hCA IIs [T = 0 s, 50 s, 3 min, and 10 min] during the "slow" release of CO2 Two active site waters, WDW (deep water) and WDW' (this study), replace the vacated space created on CO2 release, and another water, WI (intermediate water), is seen to translocate to the proton wire position W1. In addition, on the rim of the active site pocket, a water W2' (this study), in close proximity to residue His64 and W2, gradually exits the active site, whereas His64 concurrently rotates from pointing away ("out") to pointing toward ("in") active site rotameric conformation. This study provides for the first time, to our knowledge, structural "snapshots" of hCA II intermediate states during the formation of the His64-mediated proton wire that is induced as CO2 is released. Comparison of the holo- and apo-hCA II structures shows that the solvent network rearrangements require the presence of the zinc ion.