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(-) Description

Title :  THE STRUCTURE OF GH101 D764N MUTANT FROM STREPTOCOCCUS PNEUMONIAE TIGR4 IN COMPLEX WITH SERINYL T-ANTIGEN
 
Authors :  K. J. Gregg, M. D. L. Suits, L. Deng, D. J. Vocadlo, A. B. Boraston
Date :  16 Jun 15  (Deposition) - 02 Sep 15  (Release) - 28 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Endo-Beta-N-Acetylgalactosaminidase, Glycoside Hydrolase Family 101, Gh101, T-Antigen, Mucin Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. J. Gregg, M. D. L. Suits, L. Deng, D. J. Vocadlo, A. B. Boraston
Structural Analysis Of A Family 101 Glycoside Hydrolase In Complex With Carbohydrates Reveals Insights Into Its Mechanism.
J. Biol. Chem. V. 290 25657 2015
PubMed-ID: 26304114  |  Reference-DOI: 10.1074/JBC.M115.680470

(-) Compounds

Molecule 1 - ENDO-ALPHA-GALACTOSAMINIDASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 317-1426
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4
    Synonym: SPGH101

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 40)

Asymmetric/Biological Unit (7, 40)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2CA3Ligand/IonCALCIUM ION
3CIT2Ligand/IonCITRIC ACID
4EDO31Ligand/Ion1,2-ETHANEDIOL
5GAL1Ligand/IonBETA-D-GALACTOSE
6MN1Ligand/IonMANGANESE (II) ION
7SER1Mod. Amino AcidSERINE

(-) Sites  (39, 39)

Asymmetric Unit (39, 39)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:577 , ASN A:579 , ASP A:581 , ASN A:583 , ASP A:588 , HOH A:3454BINDING SITE FOR RESIDUE CA A2427
02AC2SOFTWAREGLU A:703 , ASP A:728 , HIS A:1258 , HOH A:3613 , HOH A:3715 , HOH A:3716BINDING SITE FOR RESIDUE MN A2428
03AC3SOFTWAREASP A:1233 , GLU A:1235 , GLU A:1281 , TRP A:1284 , ASP A:1411 , HOH A:4443BINDING SITE FOR RESIDUE CA A2429
04AC4SOFTWAREGLY A:1063 , ASN A:1090 , ASP A:1091 , ASP A:1207 , HOH A:4188 , HOH A:4189BINDING SITE FOR RESIDUE CA A2430
05AC5SOFTWARETHR A:1162 , ARG A:1163 , ARG A:1164 , HOH A:4354 , HOH A:4363 , HOH A:4364 , HOH A:4365 , HOH A:4464 , HOH A:4638 , HOH A:4639 , HOH A:4640 , HOH A:4641BINDING SITE FOR RESIDUE CIT A2431
06AC6SOFTWARESER A:1127 , ASN A:1128 , GLY A:1200 , ASP A:1201 , GLU A:1202 , HOH A:4289BINDING SITE FOR RESIDUE CIT A2432
07AC7SOFTWAREGLU A:796 , TRP A:797 , TRP A:810 , A2G A:2434 , HOH A:3848 , HOH A:4643 , HOH A:4645 , HOH A:4646BINDING SITE FOR RESIDUE SER A2435
08AC8SOFTWAREGLN A:462 , THR A:463 , ASP A:505 , LYS A:506 , HOH A:3217 , HOH A:4647BINDING SITE FOR RESIDUE EDO A2436
09AC9SOFTWAREASP A:1233 , ASN A:1412 , LEU A:1413 , GLN A:1414 , HOH A:4447 , HOH A:4623BINDING SITE FOR RESIDUE EDO A2437
10BC1SOFTWAREGLU A:323 , SER A:1324 , ASP A:1325 , ASN A:1391 , ARG A:1393 , HOH A:4553BINDING SITE FOR RESIDUE EDO A2438
11BC2SOFTWARELYS A:607 , HIS A:835 , GLN A:891 , HOH A:4649BINDING SITE FOR RESIDUE EDO A2439
12BC3SOFTWAREASN A:417 , ASP A:1187 , HOH A:4313 , HOH A:4650BINDING SITE FOR RESIDUE EDO A2440
13BC4SOFTWAREASP A:482 , LYS A:495 , HOH A:3274BINDING SITE FOR RESIDUE EDO A2441
14BC5SOFTWARELYS A:556 , HOH A:4651 , HOH A:4652 , HOH A:4653BINDING SITE FOR RESIDUE EDO A2442
15BC6SOFTWARELYS A:635 , TYR A:873 , ASP A:1013 , LYS A:1085 , ALA A:1089 , ASP A:1091 , EDO A:2456BINDING SITE FOR RESIDUE EDO A2443
16BC7SOFTWAREHIS A:639 , ASN A:874 , LEU A:1011 , GLN A:1037 , PRO A:1038 , HOH A:4654BINDING SITE FOR RESIDUE EDO A2444
17BC8SOFTWARESER A:336 , ASP A:416 , GLY A:1185 , HOH A:3189 , HOH A:4656BINDING SITE FOR RESIDUE EDO A2445
18BC9SOFTWARETHR A:382 , GLU A:392BINDING SITE FOR RESIDUE EDO A2446
19CC1SOFTWAREGLY A:362 , GLN A:363 , VAL A:364 , GLN A:365 , SER A:457 , GLU A:534 , VAL A:536 , TYR A:541BINDING SITE FOR RESIDUE EDO A2447
20CC2SOFTWARETYR A:1179 , PHE A:1181 , VAL A:1237 , ALA A:1238 , GLN A:1239 , PHE A:1242 , HOH A:4421BINDING SITE FOR RESIDUE EDO A2448
21CC3SOFTWAREPRO A:702 , ASP A:728 , GLN A:729 , ASP A:1278 , LYS A:1287 , PHE A:1402 , HOH A:3711 , HOH A:4508BINDING SITE FOR RESIDUE EDO A2449
22CC4SOFTWARETYR A:853 , ALA A:882 , GLN A:958 , HOH A:3967 , HOH A:3968 , HOH A:4058BINDING SITE FOR RESIDUE EDO A2450
23CC5SOFTWAREASN A:417 , GLN A:418 , VAL A:573 , SER A:595 , HOH A:3440BINDING SITE FOR RESIDUE EDO A2451
24CC6SOFTWAREPHE A:450 , ASN A:453 , HIS A:545 , SER A:546 , HOH A:3049BINDING SITE FOR RESIDUE EDO A2452
25CC7SOFTWAREGLN A:413 , ASN A:1114 , THR A:1183 , EDO A:2455 , HOH A:4658BINDING SITE FOR RESIDUE EDO A2453
26CC8SOFTWARETRP A:512 , LYS A:571 , ILE A:596 , MET A:597 , HOH A:3429 , HOH A:4660BINDING SITE FOR RESIDUE EDO A2454
27CC9SOFTWAREGLN A:413 , HIS A:420 , ASP A:422 , ASN A:1114 , EDO A:2453 , HOH A:3135 , HOH A:3437BINDING SITE FOR RESIDUE EDO A2455
28DC1SOFTWAREALA A:1089 , EDO A:2443 , HOH A:3567 , HOH A:3943 , HOH A:4238 , HOH A:4661 , HOH A:4662BINDING SITE FOR RESIDUE EDO A2456
29DC2SOFTWAREGLN A:1020 , LEU A:1022 , THR A:1030 , ASP A:1032 , HOH A:4147BINDING SITE FOR RESIDUE EDO A2457
30DC3SOFTWARETHR A:1073 , LYS A:1107 , HOH A:4390BINDING SITE FOR RESIDUE EDO A2458
31DC4SOFTWAREGLY A:522 , ASP A:525 , HIS A:799 , HOH A:3352 , HOH A:4665 , HOH A:4666BINDING SITE FOR RESIDUE EDO A2459
32DC5SOFTWARETYR A:889 , ASN A:929 , LEU A:952 , ASN A:968 , TRP A:969 , HOH A:4063BINDING SITE FOR RESIDUE EDO A2460
33DC6SOFTWARETYR A:563 , LYS A:784 , LYS A:788 , HOH A:4667 , HOH A:4668 , HOH A:4669BINDING SITE FOR RESIDUE EDO A2461
34DC7SOFTWAREHOH A:4199 , HOH A:4670BINDING SITE FOR RESIDUE EDO A2462
35DC8SOFTWAREASN A:637 , ASP A:641 , GLY A:642 , PRO A:1049 , HOH A:4126BINDING SITE FOR RESIDUE EDO A2463
36DC9SOFTWARETRP A:1358 , THR A:1359 , ASP A:1360 , SER A:1361 , LYS A:1362BINDING SITE FOR RESIDUE EDO A2464
37EC1SOFTWAREASP A:959 , THR A:993 , THR A:994 , HOH A:4055 , HOH A:4099BINDING SITE FOR RESIDUE EDO A2465
38EC2SOFTWAREASN A:1388 , ALA A:1389 , HOH A:3012 , HOH A:4672BINDING SITE FOR RESIDUE EDO A2466
39EC3SOFTWAREMET A:616 , PHE A:618 , HIS A:657 , ASP A:658 , GLU A:699 , TRP A:724 , TRP A:726 , ASN A:764 , VAL A:765 , GLU A:796 , TRP A:867 , GLN A:868 , ASP A:1254 , SER A:2435 , HOH A:3524 , HOH A:3587 , HOH A:3588 , HOH A:3852 , HOH A:3948 , HOH A:4356 , HOH A:4643 , HOH A:4644BINDING SITE FOR POLY-SACCHARIDE RESIDUES GAL A2433 THROUGH A2G A2434 BOUND TO SER A2435

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A58)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asn A:488 -Pro A:489
2Phe A:1242 -Pro A:1243
3Asp A:1264 -Pro A:1265

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A58)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A58)

(-) Exons   (0, 0)

(no "Exon" information available for 5A58)

(-) 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:1107
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeee...eeeeee.....eeeeee..eeee........eee..eee..eeeeeeee..eeeeeeeeeehhhheeeeeeeeeeee..eeeeeeeeeee...........hhhhh..eee......eeee......eeeee..........eeeee........eeee.eeeee....eeeeee.......hhhhh...eeeeeeee..eeeeeeee..ee...ee..ee.hhhhh...eeeeeee.........hhhhhhhhhh.......hhhhhh.eeeeeeee........hhhhhhhhhhhhhhhh...eeeeeee.....................hhhhhhhhhhhhhh...eeeeeeee..ee.......hhhh..........eeee...eeee.hhhhhhhhhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhh..eeee............hhhhhh............hhhhhhhhhhhh......hhhhhhhhh..............hhhh.hhhhhhhhhhhhhhhhhhhh..eeeeeee...eeeee..eeeee..eeeeeee.....eeeeee......hhhhh.eeeee..eeeee..eeeeee.........hhhhheeeeee.....eeee.hhhhhh..eeeeeee..eeeeeeee.....eeee.......eeee..............................eee.hhh.eeeee.....eeeee......eeeeee........eeeeeeeeee.....eeeeee....eeeeee................hhhhh........eeeeeeee........eeeeee......eeeeeeeeee................eee...........eee..........eeeee........hhhhh.........eeeee.......eeeeee...........eeeeeeeeee.....eeeeeee..........eeee...........eeeeeeee......eeeeeee..........hhhhhhhhh...eeeeeeeeeee..hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5a58 A  316 MEKETGPEVDDSKVTYDTIQSKVLKAVIDQAFPRVKEYSLNGHTLPGQVQQFNQVFINNHRITPEVTYKKINETTAEYLMKLRDDAHLINAEMTVRLQVVDNQLHFDVTKIVNHNQVTPGQKIDDESKLLSSISFLGNALVSVSSDQTGAKFDGATMSNNTHVSGDDHIDVTNPMKDLAKGYMYGFVSTDKLAAGVWSNSQNSYGGGSNDWTRLTAYKETVGNANYVGIHSSEWQWEKAYKGIVFPEYTKELPSAKVVITEDANADKNVDWQDGAIAYRSIMNNPQGWEKVKDITAYRIAMNFGSQAQNPFLMTLDGIKKINLHTDGLGQGVLLKGYGSEGHDSGHLNYADIGKRIGGVEDFKTLIEKAKKYGAHLGIHVNASETYPESKYFNEKILRKNPDGSYSYGWNWLDQGINIDAAYDLAHGRLARWEDLKKKLGDGLDFIYVNVWGNGQSGDNGAWATHVLAKEINKQGWRFAIEWGHGGEYDSTFHHWAADLTYGGYTNKGINSAITRFIRNHQKDAWVGDYRSYGGAANYPLLGGYSMKDFEGWQGRSDYNGYVTNLFAHDVMTKYFQHFTVSKWENGTPVTMTDNGSTYKWTPEMRVELVDADNNKVVVTRKSNDVNSPQYRERTVTLNGRVIQDGSAYLTPWNWDANGKKLSTDKEKMYYFNTQAGATTWTLPSDWAKSKVYLYKLTDQGKTEEQELTVKDGKITLDLLANQPYVLYRSKQTNPEMSWSEGMHIYDQGFNSGTLKHWTISGDASKAEIVKSQGANDMLRIQGNKEKVSLTQKLTGLKPNTKYAVYVGVDNRSNAKASITVNTGEKEVTTYTNKSLALNYVKAYAHNTRRNNATVDDTSYFQNMYAFFTTGADVSNVTLTLSREAGDEATYFDEIRTFENNSSMYGDKHDTGKGTFKQDFENVAQGIFPFVVGGVEGVEDNRTHLSEKHDPYTQRGWNGKKVDDVIEGNWSLKTNGLVSRRNLVYQTIPQNFRFEAGKTYRVTFEYEAGSDNTYAFVVGKGEFQSQASNLEMHELPNTWTDSKKAKKATFLVTGAETGDTWVGIYSTGNASNTRGDSGGNANFRGYNDFMMDNLQIEEITLTGKMLTS 2435
                                   325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295      1305      1315      1325      1335   || 1350      1360      1370      1380      1390      1400      1410      1420     ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        1339|                                                                             1426|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         1345                                                                              2435
   Legend:   → Mismatch (orange background)
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  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 5A58)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A58)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A58)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  5a58
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 Related Entries

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

UniProtKB/Swiss-Prot
        GH101_STRPN | Q2MGH6: 5a55 5a56 5a57 5a59 5a5a

(-) Related Entries Specified in the PDB File

5a55 THE NATIVE STRUCTURE OF GH101 FROM STREPTOCOCCUS PNEUMONIAE TIGR4
5a56 THE STRUCTURE OF GH101 FROM STREPTOCOCCUS PNEUMONIAE TIGR4 IN COMPLEX WITH 1-O-METHYL-T-ANTIGEN
5a57 THE STRUCTURE OF GH101 FROM STREPTOCOCCUS PNEUMONIAE TIGR4 IN COMPLEX WITH PUGT
5a59 THE STRUCTURE OF GH101 E796Q MUTANT FROM STREPTOCOCCUS PNEUMONIAE TIGR4 IN COMPLEX WITH T-ANTIGEN
5a5a THE STRUCTURE OF GH101 E796Q MUTANT FROM STREPTOCOCCUS PNEUMONIAE TIGR4 IN COMPLEX WITH PNP-T-ANTIGEN