1BWD

INOSAMINE-PHOSPHATE AMIDINOTRANSFERASE STRB1 FROM STREPTOMYCES GRISEUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.197 

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This is version 1.5 of the entry. See complete history


Literature

Crystal structure of L-arginine:inosamine-phosphate amidinotransferase StrB1 from Streptomyces griseus: an enzyme involved in streptomycin biosynthesis.

Fritsche, E.Bergner, A.Humm, A.Piepersberg, W.Huber, R.

(1998) Biochemistry 37: 17664-17672

  • DOI: 10.1021/bi981949p
  • Primary Citation of Related Structures:  
    1BWD

  • PubMed Abstract: 
  • Inosamine-phosphate amidinotransferases catalyze two nonconsecutive transamidination reactions in the biosynthesis of the streptomycin family of antibiotics. L-Arginine:inosamine-phosphate amidinotransferase StrB1 from Streptomyces griseus (StrB1) was cloned as an N-terminal hexa-histidine fusion protein, purified by affinity chromatography, and crystallized, and its crystal structure was solved by Patterson search methods at 3 ...

    Inosamine-phosphate amidinotransferases catalyze two nonconsecutive transamidination reactions in the biosynthesis of the streptomycin family of antibiotics. L-Arginine:inosamine-phosphate amidinotransferase StrB1 from Streptomyces griseus (StrB1) was cloned as an N-terminal hexa-histidine fusion protein, purified by affinity chromatography, and crystallized, and its crystal structure was solved by Patterson search methods at 3.1 A resolution. The structure is composed of five betabeta alphabeta-modules which are arranged circularly into a pseudo-5-fold symmetric particle. The three-dimensional structure is closely related to the structure of human L-arginine:glycine amidinotransferase (AT), but five loops (the 40-, 170-, 220-, 250-, and 270-loop) are organized very differently. The major changes are found in loops around the active site which open the narrow active site channel of AT to form an open and solvent-exposed cavity. In particular, module II of StrB1 is AT-like but lacks a 10-residue alpha-helix in the 170-loop. The concomitant reorganization of neighboring surface loops that surround the active site, i.e., the 40-loop and the 270-loop, results in an arrangement of loops which allows an unrestricted access of substrates to the cavity. However, the residues which are involved in substrate binding and catalysis are conserved in AT and StrB1 and are at equivalent topological positions, suggesting a similar reaction mechanism among amidinotransferases. The binding site for L-arginine had been deduced from its complex with AT. Molecular modeling revealed a possible binding mode for the second substrate scyllo-inosamine 4-phosphate.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung für Strukturforschung, Martinsried, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (INOSAMINE-PHOSPHATE AMIDINOTRANSFERASE)A, B348Streptomyces griseusMutation(s): 1 
Gene Names: strB1ATstrB
EC: 2.1.4.2
UniProt
Find proteins for P08078 (Streptomyces griseus)
Explore P08078 
Go to UniProtKB:  P08078
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08078
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.197 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.3α = 90
b = 121.3β = 90
c = 63.74γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
ROTAVATAdata scaling
TRUNCATEdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 1.4: 2019-12-11
    Changes: Advisory, Database references, Derived calculations
  • Version 1.5: 2021-11-03
    Changes: Advisory, Database references