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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ACTIVE FORM OF GALNAC-T2 IN COMPLEX WITH UDP AND THE GLYCOPEPTIDE MUC5AC-13
 
Authors :  E. Lira-Navarrete, M. Delasrivas, I. Companon, M. C. Pallares, Y. Kong J. Iglesias-Fernandez, G. J. L. Bernardes, J. M. Peregrina, C. Rovira P. Bernado, P. Bruscolini, H. Clausen, A. Lostao, F. Corzana, R. Hurtado-Guerrero
Date :  26 Feb 15  (Deposition) - 11 Mar 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Galnac-T2, Afm, Saxs, Lectin Domain, Coarse-Grained Model, Glycopeptides, Inactive Form, Active Form, Compact Form, Extended Form (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Lira-Navarrete, M. De Las Rivas, I. Companon, M. C. Pallares, Y. Kong, J. Iglesias-Fernandez, G. J. L. Bernardes, J. M. Peregrina, C. Rovira, P. Bernado, P. Bruscolini, H. Clausen, A. Lostao, F. Corzana, R. Hurtado-Guerrero
Dynamic Interplay Between Catalytic And Lectin Domains Of Galnac-Transferases Modulates Protein O-Glycosylation.
Nat. Commun. V. 6 6937 2015
PubMed-ID: 25939779  |  Reference-DOI: 10.1038/NCOMMS7937

(-) Compounds

Molecule 1 - POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2
    Chains: A
    EC Number: 2.4.1.41
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Strain: SMD1168
    Expression System Taxid: 4922
    Expression System Vector: PPICZALPHAA
    Mutation: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POLYPEPTIDE GALNAC TRANSFERASE 2, GALNAC-T2, PP-GANTASE 2, PROTEIN-UDP ACETYLGALACTOSAMINYLTRANSFERASE 2, UDP-GALNAC:POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2, POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE 2 SOLUBLE FORM
 
Molecule 2 - MUCIN
    Chains: B
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Strain: SMD1168
    Expression System Taxid: 4922
    Expression System Vector: PPICZALPHAA
    Fragment: RESIDUES 65-79
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 24)

Asymmetric/Biological Unit (4, 24)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2MN1Ligand/IonMANGANESE (II) ION
3SO421Ligand/IonSULFATE ION
4UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:143 , PHE A:144 , HIS A:145 , ASP A:176 , ARG A:201 , GLY A:203 , LEU A:204 , ASP A:224 , SER A:225 , HIS A:226 , VAL A:330 , TRP A:331 , HIS A:359 , ARG A:362 , TYR A:367 , MN A:1572 , HOH A:2146 , HOH A:2257 , HOH A:2391 , HOH A:2394 , PRO B:4 , SER B:5BINDING SITE FOR RESIDUE UDP A1570
02AC2SOFTWAREMET A:91 , ASP A:501 , ARG A:502 , HOH A:2067 , HOH A:2521 , HOH A:2523BINDING SITE FOR RESIDUE SO4 A1571
03AC3SOFTWAREASP A:224 , HIS A:226 , HIS A:359 , UDP A:1570 , HOH A:2257BINDING SITE FOR RESIDUE MN A1572
04AC4SOFTWAREHIS A:145 , ASN A:146 , ARG A:201 , TYR A:367 , THR A:368 , SO4 A:1591 , HOH A:2143 , HOH A:2403 , HOH A:2586BINDING SITE FOR RESIDUE SO4 A1573
05AC5SOFTWAREGLU A:243 , ASP A:244 , ARG A:245 , HOH A:2275 , HOH A:2276 , HOH A:2587 , HOH A:2588BINDING SITE FOR RESIDUE SO4 A1574
06AC6SOFTWAREILE A:525 , GLU A:526 , GLY A:527 , HOH A:2541BINDING SITE FOR RESIDUE SO4 A1575
07AC7SOFTWAREHIS A:123 , ARG A:293 , PRO A:297 , HOH A:2309 , HOH A:2355 , HOH A:2361 , HOH A:2589BINDING SITE FOR RESIDUE SO4 A1576
08AC8SOFTWAREGLU A:191 , LYS A:192 , HOH A:2173 , HOH A:2194 , HOH A:2590 , HOH A:2591 , HOH A:2592BINDING SITE FOR RESIDUE SO4 A1577
09AC9SOFTWAREARG A:210 , HOH A:2236 , HOH A:2593BINDING SITE FOR RESIDUE SO4 A1578
10BC1SOFTWAREARG A:132 , VAL A:133 , ASP A:134 , LYS A:161 , LYS A:162 , SO4 A:1580 , HOH A:2156 , HOH A:2160 , HOH A:2263BINDING SITE FOR RESIDUE SO4 A1579
11BC2SOFTWAREALA A:117 , ARG A:132 , LYS A:161 , SO4 A:1579 , HOH A:2077 , HOH A:2091 , HOH A:2126 , HOH A:2157 , HOH A:2160BINDING SITE FOR RESIDUE SO4 A1580
12BC3SOFTWARESER A:267 , ARG A:543 , HOH A:2309 , HOH A:2578 , HOH A:2579BINDING SITE FOR RESIDUE SO4 A1581
13BC4SOFTWAREARG A:77 , ALA A:137 , LYS A:169 , HOH A:2006 , HOH A:2135 , HOH A:2167 , HOH A:2594BINDING SITE FOR RESIDUE SO4 A1582
14BC5SOFTWAREARG A:93 , GLN A:96 , ARG A:543 , HOH A:2028BINDING SITE FOR RESIDUE SO4 A1583
15BC6SOFTWAREARG A:240 , ARG A:247 , LYS A:302 , HOH A:2270BINDING SITE FOR RESIDUE SO4 A1584
16BC7SOFTWARETYR A:284 , LYS A:546 , HOH A:2335 , HOH A:2337 , HOH A:2507 , HOH A:2508 , SER B:14 , ALA B:15 , HOH B:2009BINDING SITE FOR RESIDUE SO4 A1585
17BC8SOFTWAREARG A:532 , HOH A:2554 , HOH A:2595BINDING SITE FOR RESIDUE SO4 A1586
18BC9SOFTWARETHR A:368 , PHE A:369 , SER A:373 , HOH A:2404BINDING SITE FOR RESIDUE SO4 A1587
19CC1SOFTWARECYS A:513 , ARG A:514 , GLU A:515BINDING SITE FOR RESIDUE SO4 A1588
20CC2SOFTWAREARG A:382 , HOH A:2434 , HOH A:2435BINDING SITE FOR RESIDUE SO4 A1589
21CC3SOFTWAREPRO A:370 , GLY A:371BINDING SITE FOR RESIDUE SO4 A1592
22CC4SOFTWAREPRO A:401 , ASN A:528 , LYS A:564 , ASN A:568 , HOH A:2426 , HOH A:2596BINDING SITE FOR RESIDUE SO4 A1590
23CC5SOFTWAREHIS A:145 , TYR A:177 , ARG A:201 , THR A:368 , SO4 A:1573 , HOH A:2356BINDING SITE FOR RESIDUE SO4 A1591
24CC6SOFTWAREASP A:458 , LEU A:460 , HIS A:474 , GLY A:478 , ASN A:479 , HOH A:2500 , SER B:11 , THR B:13 , SER B:14 , ALA B:15 , HOH B:2011BINDING SITE FOR MONO-SACCHARIDE A2G B 17 BOUND TO THR B 13

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:126 -A:354
2A:345 -A:423
3A:456 -A:473
4A:496 -A:513
5A:539 -A:555

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:308 -Gly A:309

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AJP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AJP)

(-) Exons   (0, 0)

(no "Exon" information available for 5AJP)

(-) 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:495
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...............hhhhhhhh..........hhhhhhh........eeeeeee...hhhhhhhhhhhhhhhhhhh.eeeeeeee.....hhhhhhhhh...eeeee....hhhhhhhhhhhhhh...eeee....eee....hhhhhhhhhhh..eeeeeeeeee......ee.....eeeee.....eeeee.hhhhhhhhhhh....ee........eeeehhhhhhh...........hhhhhhhhhhhhh..eeeeeeeeeeee............hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh............eeeeeee..eeee..........eeee....hhhhheee.....eee..eeee..........eeee....hhhh.eeee....eeee....eeee..hhhhh..eeee...hhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ajp A  75 KVRWPDFNQEAYVGGTMVRSGQDPYARNKFNQVESDKLRMDRAIPDTRHDQCQRKQWRVDLPATSVVITFHNEARSALLRTVVSVLKKSPPHLIKEIILVDDYSNDPEDGALLGKIEKVRVLRNDRREGLMRSRVRGADAAQAKVLTFLDSHCECNEHWLEPLLERVAEDRTRVVSPIIDVINMDNFQYVGASADLKGGFDWNLVFKWDYMTPEQRRSRQGNPVAPIKTPMIAGGLFVMDKFYFEELGKYDMMMDVWGGENLEISFRVWQCGGSLEIIPCSRVGHVFRKQHPYTFPGGSGTVFARNTRRAAEVWMDEYKNFYYAAVPSARNVPYGNIQSRLELRKKLSCKPFKWYLENVYPELRVPDHQDIAFGALQQGTNCLDTLGHFADGVVGVYECHNAGGNQEWALTKEKSVKHMDLCLTVVDRAPGSLIKLQGCREDDSRQKWEQIEGNSKLRHVGSNLCLDSRTAKSGGLSVEVCGPALSQQWKFTLNL 569
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564     


Chain B from PDB  Type:PROTEIN  Length:15
                                               
               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
                 5ajp B   2 TTPSPVPTTSTTSAA  16
                                    11
   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 5AJP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AJP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AJP)

(-) Gene Ontology  (31, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        GALT2_HUMAN | Q10471: 2ffu 2ffv 4d0t 4d0z 4d11 5ajn 5ajo 5fv9
        MUC5A_HUMAN | P98088: 5ajn 5ajo
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(-) Related Entries Specified in the PDB File

5ajn CRYSTAL STRUCTURE OF THE INACTIVE FORM OF GALNAC-T2 IN COMPLEX WITH THE GLYCOPEPTIDE MUC5AC-CYS13
5ajo CRYSTAL STRUCTURE OF THE INACTIVE FORM OF GALNAC-T2 IN COMPLEX WITH THE GLYCOPEPTIDE MUC5AC-3,13