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PDBsum entry 3kyd
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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
3kyd

 

 

 

 

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Contents
Protein chains
301 a.a. *
477 a.a. *
77 a.a. *
Ligands
EDO ×3
VMX
Metals
_ZN
Waters ×215
* Residue conservation analysis
PDB id:
3kyd
Name: Ligase
Title: Human sumo e1~sumo1-amp tetrahedral intermediate mimic
Structure: Sumo-activating enzyme subunit 1. Chain: a. Synonym: ubiquitin-like 1-activating enzyme e1a. Engineered: yes. Sumo-activating enzyme subunit 2. Chain: b. Synonym: ubiquitin-like 1-activating enzyme e1b, anthracycline- associated resistance arx. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: aos1, sae1, sua1, uble1a. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: hrihfb2115, sae2, uba2, uble1b. Gene: ok/sw-cl.43, smt3c, smt3h3, sumo1, ubl1.
Resolution:
2.61Å     R-factor:   0.230     R-free:   0.284
Authors: C.D.Lima
Key ref: S.K.Olsen et al. (2010). Active site remodelling accompanies thioester bond formation in the SUMO E1. Nature, 463, 906-912. PubMed id: 20164921
Date:
05-Dec-09     Release date:   16-Feb-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9UBE0  (SAE1_HUMAN) -  SUMO-activating enzyme subunit 1 from Homo sapiens
Seq:
Struc: 		346 a.a.
301 a.a.
Protein chain
Pfam   ArchSchema ?
Q9UBT2  (SAE2_HUMAN) -  SUMO-activating enzyme subunit 2 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		640 a.a.
477 a.a.
Protein chain
Pfam   ArchSchema ?
P63165  (SUMO1_HUMAN) -  Small ubiquitin-related modifier 1 from Homo sapiens
Seq:
Struc: 		101 a.a.
77 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chain B: E.C.2.3.2.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Nature 463:906-912 (2010)
PubMed id: 20164921  
 
 
Active site remodelling accompanies thioester bond formation in the SUMO E1.
S.K.Olsen, A.D.Capili, X.Lu, D.S.Tan, C.D.Lima.
 
  ABSTRACT  
 
E1 enzymes activate ubiquitin (Ub) and ubiquitin-like (Ubl) proteins in two steps by carboxy-terminal adenylation and thioester bond formation to a conserved catalytic cysteine in the E1 Cys domain. The structural basis for these intermediates remains unknown. Here we report crystal structures for human SUMO E1 in complex with SUMO adenylate and tetrahedral intermediate analogues at 2.45 and 2.6 A, respectively. These structures show that side chain contacts to ATP.Mg are released after adenylation to facilitate a 130 degree rotation of the Cys domain during thioester bond formation that is accompanied by remodelling of key structural elements including the helix that contains the E1 catalytic cysteine, the crossover and re-entry loops, and refolding of two helices that are required for adenylation. These changes displace side chains required for adenylation with side chains required for thioester bond formation. Mutational and biochemical analyses indicate these mechanisms are conserved in other E1s.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22382979 A.A.Armstrong, F.Mohideen, and C.D.Lima (2012).
Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2.
  Nature, 483, 59-63.
PDB codes: 3v60 3v61 3v62
23142976 S.E.Kaiser, K.Mao, A.M.Taherbhoy, S.Yu, J.L.Olszewski, D.M.Duda, I.Kurinov, A.Deng, T.D.Fenn, D.J.Klionsky, and B.A.Schulman (2012).
Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures.
  Nat Struct Mol Biol, 19, 1242-1249.
PDB codes: 4gsj 4gsk 4gsl
21518904 R.N.Gilbreth, K.Truong, I.Madu, A.Koide, J.B.Wojcik, N.S.Li, J.A.Piccirilli, Y.Chen, and S.Koide (2011).
Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design.
  Proc Natl Acad Sci U S A, 108, 7751-7756.
PDB code: 3qht
22056771 S.B.Hong, B.W.Kim, K.E.Lee, S.W.Kim, H.Jeon, J.Kim, and H.K.Song (2011).
Insights into noncanonical E1 enzyme activation from the structure of autophagic E1 Atg7 with Atg8.
  Nat Struct Mol Biol, 18, 1323-1330.
PDB codes: 3rui 3ruj
21174150 Y.Song, V.Madahar, and J.Liao (2011).
Development of FRET assay into quantitative and high-throughput screening technology platforms for protein-protein interactions.
  Ann Biomed Eng, 39, 1224-1234.  
20164915 B.A.Schulman, and A.L.Haas (2010).
Structural biology: Transformative encounters.
  Nature, 463, 889-890.  
20399179 D.Völler, and H.Schindelin (2010).
And yet it moves: active site remodeling in the SUMO E1.
  Structure, 18, 419-421.  
21102611 J.R.Gareau, and C.D.Lima (2010).
The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition.
  Nat Rev Mol Cell Biol, 11, 861-871.  
21209884 J.Wang, A.M.Taherbhoy, H.W.Hunt, S.N.Seyedin, D.W.Miller, D.J.Miller, D.T.Huang, and B.A.Schulman (2010).
Crystal structure of UBA2(ufd)-Ubc9: insights into E1-E2 interactions in Sumo pathways.
  PLoS One, 5, e15805.
PDB codes: 3ong 3onh
20946979 M.Vila-Perelló, and T.W.Muir (2010).
Biological applications of protein splicing.
  Cell, 143, 191-200.  
20099854 X.Lu, S.K.Olsen, A.D.Capili, J.S.Cisar, C.D.Lima, and D.S.Tan (2010).
Designed semisynthetic protein inhibitors of Ub/Ubl E1 activating enzymes.
  J Am Chem Soc, 132, 1748-1749.  
20544217 Y.C.Shin, B.Y.Liu, J.Y.Tsai, J.T.Wu, L.K.Chang, and S.C.Chang (2010).
Biochemical characterization of the small ubiquitin-like modifiers of Chlamydomonas reinhardtii.
  Planta, 232, 649-662.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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