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(-) Description

Title :  CRYSTAL STRUCTURE OF THE INACTIVE FORM OF GALNAC-T2 IN COMPLEX WITH THE GLYCOPEPTIDE MUC5AC-CYS13
 
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 :  1.67
Chains :  Asym./Biol. Unit :  A,P
Keywords :  Transferase, 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 Common: HUMAN
    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
 
Molecule 2 - MUCIN
    Chains: P
    Engineered: YES
    Expression System: KOMAGATAELLA PASTORIS
    Expression System Strain: SMD1168
    Expression System Taxid: 4922
    Expression System Vector: PPICZALPHAA
    Fragment: RESIDUES 65-79
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MUC5AC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 27)

Asymmetric/Biological Unit (3, 27)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2EDO14Ligand/Ion1,2-ETHANEDIOL
3SO412Ligand/IonSULFATE ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:363 , GLN A:364 , HIS A:365BINDING SITE FOR RESIDUE SO4 A1570
02AC2SOFTWAREARG A:382 , TYR A:408 , HOH A:2394BINDING SITE FOR RESIDUE SO4 A1571
03AC3SOFTWAREARG A:132 , LYS A:161 , HOH A:2065 , HOH A:2077 , HOH A:2079 , HOH A:2527 , HOH A:2528BINDING SITE FOR RESIDUE SO4 A1572
04AC4SOFTWAREARG A:116 , ALA A:117 , HOH A:2059 , HOH A:2067 , HOH A:2075 , HOH A:2529 , HOH A:2530BINDING SITE FOR RESIDUE SO4 A1573
05AC5SOFTWAREGLY A:88 , GLY A:89 , ASN A:537 , HOH A:2010 , HOH A:2011 , HOH A:2510BINDING SITE FOR RESIDUE SO4 A1574
06AC6SOFTWAREARG A:532 , HOH A:2531BINDING SITE FOR RESIDUE SO4 A1575
07AC7SOFTWARESER A:267 , ALA A:268 , ARG A:543 , HOH A:2523BINDING SITE FOR RESIDUE SO4 A1576
08AC8SOFTWAREHIS A:123 , ARG A:293 , PRO A:297 , HOH A:2302 , HOH A:2532BINDING SITE FOR RESIDUE SO4 A1577
09AC9SOFTWAREHIS A:226 , HIS A:359 , VAL A:360 , ARG A:362 , HOH A:2352 , THR P:2 , THR P:3 , PRO P:4 , SER P:5BINDING SITE FOR RESIDUE SO4 A1578
10BC1SOFTWAREGLU A:526 , GLY A:527 , HOH A:2500BINDING SITE FOR RESIDUE SO4 A1579
11BC2SOFTWAREARG A:502 , SER A:518 , ARG A:519 , HIS A:533BINDING SITE FOR RESIDUE SO4 A1596
12BC3SOFTWAREARG A:93 , ARG A:543 , HOH A:2019BINDING SITE FOR RESIDUE SO4 A1580
13BC4SOFTWAREALA A:137 , HIS A:166 , LYS A:218 , HOH A:2108 , HOH A:2109BINDING SITE FOR RESIDUE EDO A1581
14BC5SOFTWAREPRO A:370 , VAL A:400 , PRO A:401 , SER A:402 , HOH A:2388BINDING SITE FOR RESIDUE EDO A1582
15BC6SOFTWARETYR A:367 , THR A:368 , SER A:373 , HOH A:2357 , HOH A:2360 , HOH A:2535BINDING SITE FOR RESIDUE EDO A1583
16BC7SOFTWAREILE A:252 , ILE A:253 , TRP A:282 , HOH A:2250 , HOH A:2266 , PRO P:8BINDING SITE FOR RESIDUE EDO A1584
17BC8SOFTWAREASP A:199 , ALA A:299 , PRO A:300 , HOH A:2310BINDING SITE FOR RESIDUE EDO A1585
18BC9SOFTWARESER A:542 , ARG A:543 , THR A:544 , ALA A:545 , LYS A:546 , HOH A:2513BINDING SITE FOR RESIDUE EDO A1586
19CC1SOFTWAREASP A:325 , MET A:326 , SER A:413 , ARG A:414 , HOH A:2326 , HOH A:2330BINDING SITE FOR RESIDUE EDO A1587
20CC2SOFTWAREGLN A:452 , SER A:542 , LEU A:559 , HOH A:2513 , HOH A:2536 , HOH P:2005BINDING SITE FOR RESIDUE EDO A1588
21CC3SOFTWAREARG A:201BINDING SITE FOR RESIDUE EDO A1589
22CC4SOFTWAREALA A:117 , PRO A:119 , HOH A:2074 , HOH A:2258 , HOH A:2537BINDING SITE FOR RESIDUE EDO A1590
23CC5SOFTWAREASP A:244 , ARG A:247 , LYS A:302 , HOH A:2246BINDING SITE FOR RESIDUE EDO A1591
24CC6SOFTWAREARG A:210 , HOH A:2173 , HOH A:2208BINDING SITE FOR RESIDUE EDO A1592
25CC7SOFTWAREASN A:260 , GLU A:526 , GLY A:527 , SER A:529 , LYS A:564BINDING SITE FOR RESIDUE EDO A1593
26CC8SOFTWAREASP A:458 , LEU A:460 , HIS A:474 , GLY A:478 , ASN A:479 , HOH A:2458 , HOH A:2539 , SER P:11 , CYS P:13 , SER P:14 , ALA P:15BINDING SITE FOR RESIDUE A2G A1594
27CC9SOFTWAREARG A:438 , HOH A:2425 , HOH A:2477BINDING SITE FOR RESIDUE EDO A1595

(-) 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
1Phe A:369 -Pro A:370

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AJN)

(-) 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 ..hhhhhhhhhhhhhhh.............hhhhhhhh..........hhhhhhh........eeeeeee...hhhhhhhhhhhhhhhhhhh.eeeeeeee.....hhhhhhhhh...eeeee.....hhhhhhhhhhhhh...eeeee...eee...hhhhhhhhhhhh..eeeeeeeeee......ee.....eeeee.....eeeee.hhhhhhhhhhh....ee........eeeehhhhhhhh............hhhhhhhhhhh..eeeeeeeeeeee............hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhh..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
                 5ajn 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 P from PDB  Type:PROTEIN  Length:16
                                                
               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
                 5ajn P   1 GTTPSPVPTTSTCSAA  16
                                    10
   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 5AJN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 5ajo 5ajp 5fv9
        MUC5A_HUMAN | P98088: 5ajo 5ajp
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(-) Related Entries Specified in the PDB File

5ajo CRYSTAL STRUCTURE OF THE INACTIVE FORM OF GALNAC-T2 IN COMPLEX WITH THE GLYCOPEPTIDE MUC5AC-3,13
5ajp CRYSTAL STRUCTURE OF THE ACTIVE FORM OF GALNAC-T2 IN COMPLEX WITH UDP AND THE GLYCOPEPTIDE MUC5AC-13