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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SPERMINE,SPERMIDINE ACETYLTRANSFERASE IN COMPLEX WITH A BISUBSTRATE ANALOG (N1-ACETYLSPERMINE-S-COA).
 
Authors :  S. S. Hegde, J. Chandler, M. W. Vetting, M. Yu, J. S. Blanchard
Date :  23 Jan 07  (Deposition) - 05 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Acyltransferase, Acetyltransferase, Gcn5 Related N- Acetyltransferase, Polyamine Biosynthesis, Gnat, Spermine, Spermidine, Transferase, Bisubstrate (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. S. Hegde, J. Chandler, M. W. Vetting, M. Yu, J. S. Blanchard
Mechanistic And Structural Analysis Of Human Spermidine/Spermine N(1)-Acetyltransferase.
Biochemistry V. 46 7187 2007
PubMed-ID: 17516632  |  Reference-DOI: 10.1021/BI700256Z

(-) Compounds

Molecule 1 - DIAMINE ACETYLTRANSFERASE 1
    ChainsA, B
    EC Number2.3.1.57
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET-28A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSPERMINE SPERMIDINE ACETYLTRANSFERASE, SPERMIDINE/SPERMINE N(1)-ACETYLTRANSFERASE 1, SSAT, SSAT-1, PUTRESCINE ACETYLTRANSFERASE, POLYAMINE N-ACETYLTRANSFERASE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NHQ2Ligand/Ion(3R)-27-AMINO-3-HYDROXY-2,2-DIMETHYL-4,8,14-TRIOXO-12-THIA-5,9,15,19,24-PENTAAZAHEPTACOS-1-YL [(2S,3R,4S,5S)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:27 , GLU A:28 , GLU A:32 , GLU A:92 , ASP A:93 , PHE A:94 , PHE A:95 , VAL A:96 , ARG A:101 , GLY A:102 , PHE A:103 , GLY A:104 , ILE A:105 , GLY A:106 , SER A:107 , LEU A:128 , SER A:136 , PHE A:139 , TYR A:140 , HOH A:2021 , HOH A:2028 , ASP B:82 , TRP B:84 , TRP B:154 , NHQ B:1171BINDING SITE FOR RESIDUE NHQ A1171
2AC2SOFTWAREASP A:82 , TRP A:84 , TRP A:154 , NHQ A:1171 , TYR B:27 , GLU B:32 , GLU B:92 , ASP B:93 , PHE B:94 , PHE B:95 , VAL B:96 , ARG B:101 , GLY B:102 , PHE B:103 , GLY B:104 , ILE B:105 , GLY B:106 , SER B:107 , LEU B:128 , SER B:136 , PHE B:139 , TYR B:140 , HOH B:2031 , HOH B:2039BINDING SITE FOR RESIDUE NHQ B1171

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JEV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JEV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2JEV)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GNATPS51186 Gcn5-related N-acetyltransferase (GNAT) domain profile.SAT1_HUMAN4-171
 
  2A:4-170
B:4-170

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003792701aENSE00001480358X:23801290-23801534245SAT1_HUMAN1-22222A:2-22
B:2-22
21
21
1.2cENST000003792702cENSE00000893299X:23801775-2380182652SAT1_HUMAN23-40182A:23-40
B:23-40
18
18
1.2eENST000003792702eENSE00001330300X:23801917-2380200084SAT1_HUMAN40-68292A:40-68
B:40-68
29
29
1.3cENST000003792703cENSE00001292529X:23803445-23803546102SAT1_HUMAN68-102352A:68-102
B:68-102
35
35
1.3fENST000003792703fENSE00000893296X:23803637-2380367741SAT1_HUMAN102-115142A:102-115
B:102-115
14
14
1.4fENST000003792704fENSE00001917283X:23803803-23804343541SAT1_HUMAN116-171562A:116-170
B:116-170
55
55

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:169
 aligned with SAT1_HUMAN | P21673 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
           SAT1_HUMAN     2 AKFVIRPATAADCSDILRLIKELAKYEYMEEQVILTEKDLLEDGFGEHPFYHCLVAEVPKEHWTPEGHSIVGFAMYYFTYDPWIGKLLYLEDFFVMSDYRGFGIGSEILKNLSQVAMRCRCSSMHFLVAEWNEPSINFYKRRGASDLSSEEGWRLFKIDKEYLLKMATE 170
               SCOP domains d2jeva_ A: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....eeeeee.hhhhh......eeeeeeeeeeee...eeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhh..eehhhhhheeeeeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GNAT  PDB: A:4-170 UniProt: 4-171                                                                                                                                       PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:2-2Exon 1.2c         ---------------------------Exon 1.3c  PDB: A:68-102           -------------Exon 1.4f  PDB: A:116-170 UniProt: 116-171 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.2e  PDB: A:40-68      ---------------------------------Exon 1.3f     ------------------------------------------------------- Transcript 1 (2)
                 2jev A   2 AKFVIRPATAADCSDILRLIKELAKYEYMEEQVILTEKDLLEDGFGEHPFYHCLVAEVPKEHWTPEGHSIVGFAMYYFTYDPWIGKLLYLEDFFVMSDYRGFGIGSEILKNLSQVAMRCRCSSMHFLVAEWNEPSINFYKRRGASDLSSEEGWRLFKIDKEYLLKMATE 170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         

Chain B from PDB  Type:PROTEIN  Length:169
 aligned with SAT1_HUMAN | P21673 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         
           SAT1_HUMAN     2 AKFVIRPATAADCSDILRLIKELAKYEYMEEQVILTEKDLLEDGFGEHPFYHCLVAEVPKEHWTPEGHSIVGFAMYYFTYDPWIGKLLYLEDFFVMSDYRGFGIGSEILKNLSQVAMRCRCSSMHFLVAEWNEPSINFYKRRGASDLSSEEGWRLFKIDKEYLLKMATE 170
               SCOP domains d2jevb_ B: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------Acetyltransf_1-2jevB01 B:65-146                                                   ------------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------Acetyltransf_1-2jevB02 B:65-146                                                   ------------------------ Pfam domains (2)
         Sec.struct. author ...eeee.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....eeeeee.hhhhh......eeeeeeeeeeee...eeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhh...eehhhhhheeeeeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --GNAT  PDB: B:4-170 UniProt: 4-171                                                                                                                                       PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:2-2Exon 1.2c         ---------------------------Exon 1.3c  PDB: B:68-102           -------------Exon 1.4f  PDB: B:116-170 UniProt: 116-171 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) --------------------------------------Exon 1.2e  PDB: B:40-68      ---------------------------------Exon 1.3f     ------------------------------------------------------- Transcript 1 (2)
                 2jev B   2 AKFVIRPATAADCSDILRLIKELAKYEYMEEQVILTEKDLLEDGFGEHPFYHCLVAEVPKEHWTPEGHSIVGFAMYYFTYDPWIGKLLYLEDFFVMSDYRGFGIGSEILKNLSQVAMRCRCSSMHFLVAEWNEPSINFYKRRGASDLSSEEGWRLFKIDKEYLLKMATE 170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161         

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JEV)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SAT1_HUMAN | P21673)
molecular function
    GO:0008080    N-acetyltransferase activity    Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.
    GO:0004145    diamine N-acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + an alkane-alpha,omega-diamine = CoA + an N-acetyldiamine.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0006596    polyamine biosynthetic process    The chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups.
    GO:0009447    putrescine catabolic process    The chemical reactions and pathways resulting in the breakdown of putrescine, 1,4-diaminobutane; putrescine is the metabolic precursor of spermidine and spermine.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SAT1_HUMAN | P216732b3u 2b3v 2b4b 2b4d 2b58 2b5g 2f5i 2fxf 2g3t

(-) Related Entries Specified in the PDB File

2b3u HUMAN SPERMINE SPERMIDINE ACETYLTRANSFERASE K26R MUTANT
2b3v SPERMINE SPERMIDINE ACETYLTRANSFERASE IN COMPLEX WITHACETYLCOA, K26R MUTANT
2b4b SSAT+COA+BE-3-3-3, K6R MUTANT
2b4d SSAT+COA+SP- SP DISORDERED
2b58 SSAT WITH COA_SP, SPERMINE DISORDERED, K26R MUTANT
2b5g WILD TYPE SSAT- 1.7A STRUCTURE
2f5i X-RAY STRUCTURE OF SPERMIDINE/SPERMINE N1- ACETYLTRANSFERASE(SAT) FROM HOMO SAPIENS
2fxf HUMAN SPERMIDINE/SPERMINE N1-ACETYLTRANSFERASE
2g3t CRSYTAL STRUCTURE OF HUMAN SPERMIDINE/SPERMINE N1-ACETYLTRANSFERASE (HSSAT)