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(-) Description

Title :  CRYSTAL STRUCTURE OF NATD BOUND TO H4/H2A PEPTIDE AND COA
 
Authors :  R. S. Magin, G. P. Liszczak, R. Marmorstein
Date :  06 Aug 14  (Deposition) - 28 Jan 15  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,G  (1x)
Biol. Unit 4:  D,H  (1x)
Keywords :  Acetyltransferase, Gnat Fold, N-Terminal Acetylation, Acetyl-Coa, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. S. Magin, G. P. Liszczak, R. Marmorstein
The Molecular Basis For Histone H4- And H2A-Specific Amino-Terminal Acetylation By Natd.
Structure V. 23 332 2015
PubMed-ID: 25619998  |  Reference-DOI: 10.1016/J.STR.2014.10.025

(-) Compounds

Molecule 1 - N-ALPHA-ACETYLTRANSFERASE 40
    ChainsA, B, C, D
    EC Number2.3.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 17-220
    GeneNAA40, NAT11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymN-ACETYLTRANSFERASE 11,NATD CATALYTIC SUBUNIT
 
Molecule 2 - HISTONE H4/H2A N-TERMINUS
    ChainsE, F, G, H
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)A    F  
Biological Unit 2 (1x) B  E   
Biological Unit 3 (1x)  C   G 
Biological Unit 4 (1x)   D   H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
1COA4Ligand/IonCOENZYME A
2GOL4Ligand/IonGLYCEROL
3NA4Ligand/IonSODIUM ION
4NH24Mod. Amino AcidAMINO GROUP
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
2GOL2Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4NH21Mod. Amino AcidAMINO GROUP
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
2GOL-1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4NH21Mod. Amino AcidAMINO GROUP
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
2GOL1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4NH21Mod. Amino AcidAMINO GROUP
Biological Unit 4 (3, 3)
No.NameCountTypeFull Name
1COA1Ligand/IonCOENZYME A
2GOL1Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:140 , GLN A:141 , LEU A:142 , ARG A:147 , ARG A:148 , LYS A:149 , GLY A:150 , GLY A:152 , LYS A:153 , ASN A:179 , GLY A:181 , ALA A:182 , GLN A:184 , PHE A:185 , ALA A:189 , NA A:302 , HOH A:438 , HOH A:454 , HOH A:486 , GOL D:302 , SER F:1binding site for residue COA A 301
02AC2SOFTWAREGLU A:139 , VAL A:140 , GLN A:141 , COA A:301 , SER F:1binding site for residue NA A 302
03AC3SOFTWARETYR A:85 , TRP A:90 , LYS A:97 , GLU A:100 , GLY B:14 , GLY F:2 , ARG F:3binding site for residue GOL A 303
04AC4SOFTWAREGLN A:157 , GLN A:160 , HOH A:472 , HOH A:505 , GLN B:160 , ASN B:164binding site for residue GOL A 304
05AC5SOFTWAREVAL B:140 , GLN B:141 , LEU B:142 , ARG B:147 , ARG B:148 , LYS B:149 , GLY B:150 , GLY B:152 , LYS B:153 , ASN B:179 , GLY B:181 , GLN B:184 , PHE B:185 , ALA B:189 , HOH B:430 , HOH B:435 , HOH B:436 , HOH B:502 , HOH B:507 , SER E:1 , NA E:101binding site for residue COA B 301
06AC6SOFTWAREVAL C:140 , GLN C:141 , LEU C:142 , ARG C:147 , ARG C:148 , LYS C:149 , GLY C:150 , LEU C:151 , GLY C:152 , LYS C:153 , ASN C:179 , GLY C:181 , GLN C:184 , PHE C:185 , PHE C:186 , ALA C:189 , NA C:302 , HOH C:414 , HOH C:421 , HOH C:431 , HOH C:443 , SER G:1binding site for residue COA C 301
07AC7SOFTWAREGLU C:139 , VAL C:140 , GLN C:141 , COA C:301 , SER G:1binding site for residue NA C 302
08AC8SOFTWARETYR C:85 , TRP C:90 , LYS C:97 , GLU C:100 , GLY G:2 , ARG G:3binding site for residue GOL C 303
09AC9SOFTWAREVAL D:140 , GLN D:141 , LEU D:142 , ARG D:147 , ARG D:148 , LYS D:149 , GLY D:150 , GLY D:152 , LYS D:153 , ASN D:179 , GLY D:181 , GLN D:184 , PHE D:185 , ALA D:189 , HOH D:413 , HOH D:420 , HOH D:423 , HOH D:435 , HOH D:441 , SER H:1 , NA H:101binding site for residue COA D 301
10AD1SOFTWAREGLN A:184 , GLU A:188 , COA A:301 , ILE D:194 , SER D:200 , MET D:201binding site for residue GOL D 302
11AD2SOFTWAREGLU B:139 , VAL B:140 , COA B:301 , SER E:1binding site for residue NA E 101
12AD3SOFTWAREGLU D:139 , VAL D:140 , COA D:301 , SER H:1binding site for residue NA H 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U9W)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn C:114 -Ser C:115

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U9W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U9W)

(-) Exons   (0, 0)

(no "Exon" information available for 4U9W)

(-) Sequences/Alignments

Asymmetric 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:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..hhhhhhhhh.eeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...eeeeeeee..eeeeeeeeeeeee..eeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh....ee........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u9w A  16 MEERAAMDAVCAKVDAANRLGDPLEAFPVFKKYDRNGLNVSIECKRVSGLEPATVDWAFDLTKTNMQTMYEQSEWGWKDREKREEMTDDRAWYLIAWENSSVPVAFSHFRFDVECGDEVLYCYEVQLESKVRRKGLGKFLIQILQLMANSTQMKKVMLTVFKHNHGAYQFFREALQFEIDDSSPSCSYEILSRRTKF 220
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195    || 213       
                                                                                                                                                                                                                  200|           
                                                                                                                                                                                                                   209           

Chain B from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh......hhhh.ee......eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...eeeeeee....eeeeeeeeeeee..eeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh....ee.........eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u9w B  14 GSMEERAAMDAVCAKVDAANRLGDPLEAFPVFKKYDRNGLNVSIECKRVSGLEPATVDWAFDLTKTNMQTMYEQSEWGWKDREKREEMTDDRAWYLIAWENSSVPVAFSHFRFDVECGDEVLYCYEVQLESKVRRKGLGKFLIQILQLMANSTQMKKVMLTVFKHNHGAYQFFREALQFEIDDSSPSDCSYEILSRRTKF 220
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193      |210       220
                                                                                                                                                                                                                    200|            
                                                                                                                                                                                                                     208            

Chain C from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh..hhhhhhhhh.eeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...eeeeee.....eeeeeeeeeeee..eeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh....ee.........eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u9w C  19 RAAMDAVCAKVDAANRLGDPLEAFPVFKKYDRNGLNVSIECKRVSGLEPATVDWAFDLTKTNMQTMYEQSEWGWKDREKREEMTDDRAWYLIAWENSSVPVAFSHFRFDVECGDEVLYCYEVQLESKVRRKGLGKFLIQILQLMANSTQMKKVMLTVFKHNHGAYQFFREALQFEIDDSSPSDCSYEILSRRTKF 220
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198 ||    215     
                                                                                                                                                                                                               200|            
                                                                                                                                                                                                                208            

Chain D from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.......hhhh.ee......eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh....eeeeeee...eeeeeeeeeeeee..eeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhh....ee.........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4u9w D  22 MDAVCAKVDAANRLGDPLEAFPVFKKYDRNGLNVSIECKRVSGLEPATVDWAFDLTKTNMQTMYEQSEWGWKDREKREEMTDDRAWYLIAWENSSVPVAFSHFRFDVECGDEVLYCYEVQLESKVRRKGLGKFLIQILQLMANSTQMKKVMLTVFKHNHGAYQFFREALQFEIDDSSPSMCSYEILSRRTKF 220
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201|      218  
                                                                                                                                                                                                             201|           
                                                                                                                                                                                                              209           

Chain E from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4u9w E   1 SGRGKx   6
                                 |
                                 6-NH2

Chain F from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4u9w F   1 SGRGKx   6
                                 |
                                 6-NH2

Chain G from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4u9w G   1 SGRGKx   6
                                 |
                                 6-NH2

Chain H from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 4u9w H   1 SGRGKx   6
                                 |
                                 6-NH2

   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  (0, 0)

(no "SCOP Domain" information available for 4U9W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U9W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U9W)

(-) Gene Ontology  (35, 35)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        H4_HUMAN | P628051kx4 1kx5 1m18 1m19 1m1a 1s32 1zkk 2bqz 2cv5 2ig0 2kwn 2kwo 2lvm 2qqs 2rje 2rny 2rs9 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3cfs 3cfv 3f9w 3f9x 3f9y 3f9z 3ij1 3jpx 3nqj 3nqu 3o36 3qby 3qzs 3qzt 3qzv 3r45 3uvw 3uvx 3uvy 3uw9 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1u 3x1v 4gqb 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4m38 4n3w 4n4f 4qut 4quu 4qyd 4ym5 4ym6 4yy6 4yyd 4yyg 4yyh 4yyi 4yyj 4yyk 4yym 4yyn 4z2m 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b2j 5b31 5b32 5b33 5b40 5bnv 5bnx 5bo0 5c3i 5cpi 5cpj 5cpk 5fa5 5ffw 5fwe 5gse 5gsu 5gt0 5gt3 5gtc 5gxq 5ja4 5jrg 5kdm 5teg 5x7x
        NAA40_HUMAN | Q86UY64u9v

(-) Related Entries Specified in the PDB File

4u9v 4u9x 4ua3