7X98 | pdb_00007x98

5-Aminolevulinate synthase HemA from Rhodopseudomonas palustris

• PDB DOI: https://doi.org/10.2210/pdb7X98/pdb

• Classification: TRANSFERASE
• Organism(s): Rhodopseudomonas palustris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-15 Released: 2023-03-08 
• Deposition Author(s): Zhang, T.T., Liu, H.P.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 5-Aminolevulinate synthase HemA from Rhodopseudomonas palustris presents multiple conformations.

Zhang, T., Chen, J., Zheng, P., Gong, W., Sun, J., Liu, H.

(2022) Biochem Biophys Res Commun 609: 100-104

• PubMed: 35427926 
• DOI: https://doi.org/10.1016/j.bbrc.2022.04.021
• Primary Citation of Related Structures:  
  7X98


• PubMed Abstract: 
  

  5-ALA is the precursor of all tetrapyrroles. 5-Aminolevulinate synthase (ALAS) catalyzes the production of 5-aminolevulinic acid (5-ALA) from glycine and succinyl-CoA. HemA from Rhodopseudomonas palustris (Rp-HemA) was reported to be a highly active ALAS. To understand the catalytic mechanism of Rp-HemA, the 2.05 Å resolution crystal structure of Rp-HemA was solved. Open, half close and close conformations were observed in the substrate-free structures. Structure comparison and sequence alignment suggest the newly observed half close conformation may also be conserved in ALAS family. The pre-existed close and half close conformations in Rp-HemA may play a key role for its high activity.

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Organizational Affiliation: 

University of Chinese Academy of Sciences, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 175.86 kDa 
• Atom Count: 13,145 
• Modelled Residue Count: 1,598 
• Deposited Residue Count: 1,612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-aminolevulinate synthase	A, B, C, D	403	Rhodopseudomonas palustris	Mutation(s): 0  Gene Names: hemA, HUU61_06935 EC: 2.3.1.37
UniProt
Find proteins for M1FRN3 (Rhodopseudomonas palustris) Explore M1FRN3  Go to UniProtKB:  M1FRN3

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.157	α = 82.02
b = 68.896	β = 85.26
c = 85.639	γ = 66.06

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-08 
Deposition Author(s): Zhang, T.T., Liu, H.P.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-03-08
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description