6CK0 | pdb_00006ck0

Crystal Structure of Biotin Acetyl Coenzyme A Carboxylase Synthetase from Helicobacter pylori with bound Biotinylated ATP

PDB DOI: https://doi.org/10.2210/pdb6CK0/pdb

Classification: LIGASE
Organism(s): Helicobacter pylori G27
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-02-27 Released: 2018-04-04
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.221 (Depositor), 0.227 (DCC)
R-Value Work:
0.171 (Depositor), 0.175 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Co-crystal structure of Helicobacter pylori biotin protein ligase with biotinyl-5-ATP.

Ayanlade, J.P., Davis, D.E., Subramanian, S., Dranow, D.M., Lorimer, D.D., Hammerson, B., Myler, P.J., Asojo, O.A.

(2025) Acta Crystallogr F Struct Biol Commun 81: 11-18

PubMed: 39704719 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X24012056
Primary Citation Related Structures:
6CK0

PubMed Abstract:
Helicobacter pylori, a type 1 carcinogen that causes human gastric ulcers and cancer, is a priority target of the Seattle Structural Genomics Center for Infectious Disease (SSGCID). These efforts include determining the structures of potential H. pylori therapeutic targets. Here, the purification, crystallization and X-ray structure of one such target, H. pylori biotin protein ligase (HpBPL), are reported. HpBPL catalyzes the activation of various biotin-dependent metabolic pathways, including fatty-acid synthesis, gluconeogenesis and amino-acid catabolism, and may facilitate the survival of H. pylori in the high-pH gastric mucosa. HpBPL is a prototypical bacterial biotin protein ligase, despite having less than 35% sequence identity to any reported structure in the Protein Data Bank. A biotinyl-5-ATP molecule sits in a well conserved cavity. HpBPL shares extensive tertiary-structural similarity with Mycobacterium tuberculosis biotin protein ligase (MtBPL), despite having less than 22% sequence identity. The active site of HpBPL is very similar to that of MtBPL and has the necessary residues to bind inhibitors developed for MtBPL.

Organizational Affiliation

Dartmouth Cancer Center, One Medical Center Drive, Lebanon, NH 03756, USA.

Macromolecule Content

Total Structure Weight: 52.13 kDa
Atom Count: 3,489
Modeled Residue Count: 419
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biotin acetyl coenzyme A carboxylase synthetase	A, B	220	Helicobacter pylori G27	Mutation(s): 0 Gene Names: HPG27_1085
UniProt
Find proteins for B5Z8D8 (Helicobacter pylori (strain G27)) Explore B5Z8D8 Go to UniProtKB: B5Z8D8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5Z8D8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F5D (Subject of Investigation/LOI) Query on F5D Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	5'-O-[(S)-({5-[(2R,3aS,4S,6aR)-2-hydroxyhexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}oxy){[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]adenosine C₂₀ H₃₂ N₇ O₁₅ P₃ S KMVPKOZRCVFEFI-NSWRTZSASA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B], H [auth B], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], K [auth B], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.221 (Depositor), 0.227 (DCC)
R-Value Work: 0.171 (Depositor), 0.175 (DCC)
R-Value Observed: 0.175 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.89	α = 122.14
b = 57.08	β = 94.73
c = 57.03	γ = 107.85

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MR-Rosetta	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-04-04

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2018-04-04
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.2: 2025-01-15
Changes: Database references, Structure summary