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PDBsum entry 1vjo

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Transferase PDB id
1vjo
Jmol
Contents
Protein chain
377 a.a. *
Ligands
PLP
Waters ×432
* Residue conservation analysis
PDB id:
1vjo
Name: Transferase
Title: Crystal structure of alanine--glyoxylate aminotransferase (a from nostoc sp. At 1.70 a resolution
Structure: Alanine--glyoxylate aminotransferase. Chain: a. Engineered: yes
Source: Nostoc sp.. Organism_taxid: 103690. Strain: pcc 7120. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
1.70Å     R-factor:   0.154     R-free:   0.202
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
G.W.Han et al. (2005). Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 A resolution reveals a noncovalently linked PLP cofactor. Proteins, 58, 971-975. PubMed id: 15657930 DOI: 10.1002/prot.20360
Date:
16-Mar-04     Release date:   23-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q8YY48  (Q8YY48_NOSS1) -  Alanine--glyoxylate aminotransferase
Seq:
Struc:
381 a.a.
377 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     4 terms  

 

 
DOI no: 10.1002/prot.20360 Proteins 58:971-975 (2005)
PubMed id: 15657930  
 
 
Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 A resolution reveals a noncovalently linked PLP cofactor.
G.W.Han, R.Schwarzenbacher, R.Page, L.Jaroszewski, P.Abdubek, E.Ambing, T.Biorac, J.M.Canaves, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, A.Godzik, C.Grittini, S.K.Grzechnik, J.Hale, E.Hampton, J.Haugen, M.Hornsby, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, S.A.Lesley, I.Levin, D.McMullan, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, E.Nigoghossian, J.Ouyang, J.Paulsen, K.Quijano, R.Reyes, E.Sims, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, F.von Delft, X.Wang, B.West, A.White, G.Wolf, Q.Xu, O.Zagnitko, K.O.Hodgson, J.Wooley, I.A.Wilson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal structure of AGT from Anabaena sp. (A) Stereo ribbon diagram of Anabena sp. AGT color-coded from N-terminus (blue) to C-terminus (red), showing the domain organization and location of the putative active site (PLP molecule shown in ball-and-stick representation). Helices H1-H15 and -strands ( 1- 12), as well as -sheets A, B, and C are indicated. (B) Diagram showing the secondary structure elements in Anabaena sp. AGT superimposed on its primary sequence. The -sheet designations are indicated by a red A, B, and C. Above each -strand, -bulges and -turns are indicated. -hairpins are depicted as red loops. Disordered regions are depicted by a dashed line, with the corresponding sequence in brackets.
Figure 2.
Figure 2. (A) Ribbon diagram of the Anabaena sp. AGT dimer. The N-terminal segment (red), N-terminal domain (green), and C-terminal domain (blue) are indicated for chain A. (B) Superposition of Anabaena sp. AGT (blue) and human AGT (PDB code: 1h0c; gray). The corresponding bound PLP and LLP (lysine-pyridoxal-5 -phosphate) ligands are shown in ball-and-stick representation, and regions of structural difference are labeled. (C) The PLP molecule bound to the active site of Anabaena sp. AGT and interacting residues are shown in ball-and-stick representation. 2Fo-Fc density for PLP contoured at 1 is shown in blue. (D) Superposition of the active sites with the PLP and LLP molecules and interacting residues from Anabaena sp. AGT (blue) and their counterparts in human AGT (gray, residues labeled in brackets) in ball-and-stick representation.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2005, 58, 971-975) copyright 2005.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19770506 S.Panjikar, V.Parthasarathy, V.S.Lamzin, M.S.Weiss, and P.A.Tucker (2009).
On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination.
  Acta Crystallogr D Biol Crystallogr, 65, 1089-1097.  
18560158 H.Sakuraba, K.Yoneda, K.Takeuchi, H.Tsuge, N.Katunuma, and T.Ohshima (2008).
Structure of an archaeal alanine:glyoxylate aminotransferase.
  Acta Crystallogr D Biol Crystallogr, 64, 696-699.
PDB code: 2zc0
17989071 Y.Yoshikane, N.Yokochi, M.Yamasaki, K.Mizutani, K.Ohnishi, B.Mikami, H.Hayashi, and T.Yagi (2008).
Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti MAFF303099.
  J Biol Chem, 283, 1120-1127.
PDB codes: 2z9u 2z9v 2z9w 2z9x
17300176 S.Lima, R.Khristoforov, C.Momany, and R.S.Phillips (2007).
Crystal structure of Homo sapiens kynureninase.
  Biochemistry, 46, 2735-2744.
PDB code: 2hzp
16990263 Q.Han, H.Robinson, Y.G.Gao, N.Vogelaar, S.R.Wilson, M.Rizzi, and J.Li (2006).
Crystal structures of Aedes aegypti alanine glyoxylate aminotransferase.
  J Biol Chem, 281, 37175-37182.
PDB codes: 2huf 2hui 2huu
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