2NZ2

Crystal structure of human argininosuccinate synthase in complex with aspartate and citrulline

• PDB DOI: https://doi.org/10.2210/pdb2NZ2/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-11-22 Released: 2006-12-05 
• Deposition Author(s): Karlberg, T., Uppenberg, J., Arrowsmith, C., Berglund, H., Busam, R.D., Collins, R., Edwards, A., Ericsson, U.B., Flodin, S., Flores, A., Graslund, S., Hallberg, B.M., Hammarstrom, M., Hogbom, M., Johansson, I., Kotenyova, T., Magnusdottir, A., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Wallden, K., Weigelt, J., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.265 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 

Starting Model: experimental

Literature

Structure of human argininosuccinate synthetase.

Karlberg, T., Collins, R., van den Berg, S., Flores, A., Hammarstrom, M., Hogbom, M., Holmberg Schiavone, L., Uppenberg, J.

(2008) Acta Crystallogr D Biol Crystallogr 64: 279-286

• PubMed: 18323623 
• DOI: https://doi.org/10.1107/S0907444907067455
• Primary Citation of Related Structures:  
  2NZ2


• PubMed Abstract: 
  

  Argininosuccinate synthetase catalyzes the transformation of citrulline and aspartate into argininosuccinate and pyrophosphate using the hydrolysis of ATP to AMP and pyrophosphate. This enzymatic process constitutes the rate-limiting step in both the urea and arginine-citrulline cycles. Previous studies have investigated the crystal structures of argininosuccinate synthetase from bacterial species. In this work, the first crystal structure of human argininosuccinate synthetase in complex with the substrates citrulline and aspartate is presented. The human enzyme is compared with structures of argininosuccinate synthetase from bacteria. In addition, the structure also provides new insights into the function of the numerous clinical mutations identified in patients with type I citrullinaemia (also known as classic citrullinaemia).

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Organizational Affiliation: 

Structural Genomics Consortium, Karolinska Institutet, MBB/SGC, 171 77 Stockholm, Sweden.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 47.01 kDa 
• Atom Count: 3,423 
• Modelled Residue Count: 402 
• Deposited Residue Count: 413 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Argininosuccinate synthase	A	413	Homo sapiens	Mutation(s): 0  Gene Names: ASS1, ASS EC: 6.3.4.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00966 (Homo sapiens) Explore P00966  Go to UniProtKB:  P00966
PHAROS:  P00966 GTEx:  ENSG00000130707

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIR	D [auth A]	CITRULLINE C6 H13 N3 O3 RHGKLRLOHDJJDR-BYPYZUCNSA-N
ASP	C [auth A]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.265 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 
• Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.94	α = 90
b = 117.47	β = 90
c = 155.15	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-05 
Deposition Author(s): Karlberg, T., Uppenberg, J., Arrowsmith, C., Berglund, H., Busam, R.D., Collins, R., Edwards, A., Ericsson, U.B., Flodin, S., Flores, A., Graslund, S., Hallberg, B.M., Hammarstrom, M., Hogbom, M., Johansson, I., Kotenyova, T., Magnusdottir, A., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Wallden, K., Weigelt, J., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-12-05
  Type: Initial release
  
• Version 1.1: 2008-02-20
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection