PDBsum entry 6zmd

Transferase

PDB id: 6zmd

Contents

Protein chains

523 a.a.

332 a.a.

Ligands

ANP

QMK

PO4 ×2

Metals

_MG ×2

Waters ×74

PDB id:

6zmd

Name:

Transferase

Title:

Crystal structure of hype covalently tethered to bip bound to amp-pnp

Structure:

Endoplasmic reticulum chaperone bip. Chain: a. Synonym: 78 kda glucose-regulated protein,grp-78,binding- immunoglobulin protein,bip,heat shock protein 70 family protein 5, hsp70 family protein 5,heat shock protein family a member 5, immunoglobulin heavy chain-binding protein. Engineered: yes. Mutation: yes. Protein adenylyltransferase ficd.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hspa5, grp78. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: ficd, hip13, hype, unq3041/pro9857. Expression_system_taxid: 562

Resolution:

2.64Å R-factor: 0.194 R-free: 0.235

Authors:

J.Fauser,B.Gulen,C.Pett,C.Hedberg,A.Itzen,V.Pogenberg

Key ref:

J.Fauser et al. Structural basis for hype mediated ampylation of the hsp70 chaperone bip. Nat commun, . PubMed id: 33893288

Date:

02-Jul-20 Release date: 14-Apr-21

Protein chain

P11021  (BIP_HUMAN) -  Endoplasmic reticulum chaperone BiP from Homo sapiens

Seq: 654 a.a.

Struc: 523 a.a.*

Protein chain

Q9BVA6  (FICD_HUMAN) -  Protein adenylyltransferase FICD from Homo sapiens

Seq: 458 a.a.

Struc: 332 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chain A: E.C.3.6.4.10 - non-chaperonin molecular chaperone ATPase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP + H2O = ADP (Bound ligand (Het Group name = ANP) matches with 81.25% similarity) + phosphate + H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

• Enzyme class 2: Chain B: E.C.2.7.7.108 - protein adenylyltransferase.
• Reaction:
  1. L-seryl-[protein] + ATP = 3-O-(5'-adenylyl)-L-seryl-[protein] + diphosphate
  2. L-threonyl-[protein] + ATP = 3-O-(5'-adenylyl)-L-threonyl-[protein] + diphosphate
  3. L-tyrosyl-[protein] + ATP = O-(5'-adenylyl)-L-tyrosyl-[protein] + diphosphate

L-seryl-[protein] (Bound ligand (Het Group name = ANP) matches with 72.22% similarity) + ATP = 3-O-(5'-adenylyl)-L-seryl-[protein] + diphosphate (Bound ligand (Het Group name = PO4) matches with 55.56% similarity)

L-threonyl-[protein] (Bound ligand (Het Group name = ANP) matches with 72.22% similarity) + ATP = 3-O-(5'-adenylyl)-L-threonyl-[protein] + diphosphate (Bound ligand (Het Group name = PO4) matches with 55.56% similarity)

L-tyrosyl-[protein] (Bound ligand (Het Group name = ANP) matches with 72.22% similarity) + ATP = O-(5'-adenylyl)-L-tyrosyl-[protein] (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + diphosphate

• Enzyme class 3: Chain B: E.C.3.1.4.- - ?????

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