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(-) Description

Title :  THE STRUCTURE OF GH101 FROM STREPTOCOCCUS PNEUMONIAE TIGR4 IN COMPLEX WITH 1-O-METHYL-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-N-ACETYLGALACTOSAMINIDASE
    Chains: A
    EC Number: 3.2.1.97
    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: RESIDUES 317-1425
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 170187
    Strain: TIGR4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 39)

Asymmetric/Biological Unit (6, 39)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CIT2Ligand/IonCITRIC ACID
3EDO31Ligand/Ion1,2-ETHANEDIOL
4GAL1Ligand/IonBETA-D-GALACTOSE
5MGC1Ligand/IonALPHA-METHYL-N-ACETYL-D-GALACTOSAMINE
6MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (37, 37)

Asymmetric Unit (37, 37)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:577 , ASN A:579 , ASP A:581 , ASN A:583 , ASP A:588 , HOH A:3413BINDING SITE FOR RESIDUE CA A2427
02AC2SOFTWAREGLU A:703 , ASP A:728 , HIS A:1258 , HOH A:3561 , HOH A:3652 , HOH A:3653BINDING SITE FOR RESIDUE MN A2428
03AC3SOFTWAREASP A:1233 , GLU A:1235 , GLU A:1281 , TRP A:1284 , ASP A:1411 , HOH A:4332BINDING SITE FOR RESIDUE CA A2429
04AC4SOFTWAREGLY A:1063 , ASN A:1090 , ASP A:1091 , ASP A:1207 , HOH A:4097 , HOH A:4098BINDING SITE FOR RESIDUE CA A2430
05AC5SOFTWARETHR A:1162 , ARG A:1163 , ARG A:1164 , HOH A:4251 , HOH A:4256 , HOH A:4257 , HOH A:4258 , HOH A:4352 , HOH A:4511 , HOH A:4512 , HOH A:4513BINDING SITE FOR RESIDUE CIT A2431
06AC6SOFTWARESER A:1127 , ASN A:1128 , GLY A:1200 , ASP A:1201 , GLU A:1202 , HOH A:4191 , HOH A:4286 , HOH A:4287 , HOH A:4514BINDING SITE FOR RESIDUE CIT A2432
07AC7SOFTWAREGLN A:462 , THR A:463 , ASP A:505 , LYS A:506 , HOH A:3193 , HOH A:4516 , HOH A:4517BINDING SITE FOR RESIDUE EDO A2465
08AC8SOFTWAREASP A:1233 , ASN A:1412 , LEU A:1413 , GLN A:1414 , HOH A:4336 , HOH A:4498 , HOH A:4518BINDING SITE FOR RESIDUE EDO A2435
09AC9SOFTWAREGLU A:323 , SER A:1324 , ASP A:1325 , ASN A:1391 , ARG A:1393 , HOH A:4433 , HOH A:4435BINDING SITE FOR RESIDUE EDO A2436
10BC1SOFTWARELYS A:607 , HIS A:835 , GLN A:891 , HOH A:4519BINDING SITE FOR RESIDUE EDO A2437
11BC2SOFTWAREASP A:416 , ASN A:417 , ASP A:1187 , HOH A:4214 , HOH A:4215 , HOH A:4520BINDING SITE FOR RESIDUE EDO A2438
12BC3SOFTWAREASP A:482 , LYS A:495 , HOH A:3251 , HOH A:3254BINDING SITE FOR RESIDUE EDO A2439
13BC4SOFTWARELYS A:556 , HOH A:4521 , HOH A:4522 , HOH A:4523BINDING SITE FOR RESIDUE EDO A2440
14BC5SOFTWARELYS A:635 , TYR A:873 , ASP A:1013 , LYS A:1085 , ALA A:1089 , ASP A:1091 , EDO A:2454 , HOH A:3520 , HOH A:3521BINDING SITE FOR RESIDUE EDO A2441
15BC6SOFTWAREHIS A:639 , ASN A:874 , GLN A:1037 , PRO A:1038 , HOH A:3529 , HOH A:4524BINDING SITE FOR RESIDUE EDO A2442
16BC7SOFTWARESER A:336 , VAL A:415 , ASP A:416 , GLY A:1185 , HOH A:3171 , HOH A:4525BINDING SITE FOR RESIDUE EDO A2443
17BC8SOFTWARETHR A:382 , GLU A:392 , LEU A:394 , HOH A:3091BINDING SITE FOR RESIDUE EDO A2444
18BC9SOFTWAREGLY A:362 , GLN A:363 , VAL A:364 , GLN A:365 , SER A:457 , GLU A:534BINDING SITE FOR RESIDUE EDO A2445
19CC1SOFTWARETYR A:1179 , PHE A:1181 , VAL A:1237 , ALA A:1238 , GLN A:1239 , PHE A:1242 , HOH A:4312BINDING SITE FOR RESIDUE EDO A2446
20CC2SOFTWAREPRO A:702 , ASP A:728 , GLN A:729 , ASP A:1278 , LYS A:1287 , HOH A:3649 , HOH A:4396BINDING SITE FOR RESIDUE EDO A2447
21CC3SOFTWARETYR A:853 , ALA A:882 , GLN A:958 , HOH A:3885 , HOH A:3886 , HOH A:3971BINDING SITE FOR RESIDUE EDO A2448
22CC4SOFTWAREASN A:417 , GLN A:418 , VAL A:573 , SER A:595 , HOH A:3401BINDING SITE FOR RESIDUE EDO A2449
23CC5SOFTWAREPHE A:450 , ASN A:453 , HIS A:545 , SER A:546 , HOH A:3047BINDING SITE FOR RESIDUE EDO A2450
24CC6SOFTWAREGLN A:413 , ASN A:1114 , THR A:1183 , EDO A:2453 , HOH A:4527BINDING SITE FOR RESIDUE EDO A2451
25CC7SOFTWARETRP A:512 , LYS A:571 , ILE A:596BINDING SITE FOR RESIDUE EDO A2452
26CC8SOFTWAREGLN A:413 , HIS A:420 , ASP A:422 , ASN A:1114 , EDO A:2451 , HOH A:3398BINDING SITE FOR RESIDUE EDO A2453
27CC9SOFTWARETYR A:873 , ALA A:1089 , EDO A:2441 , HOH A:3520 , HOH A:3859 , HOH A:4143 , HOH A:4529 , HOH A:4530BINDING SITE FOR RESIDUE EDO A2454
28DC1SOFTWAREGLN A:1020 , THR A:1030 , ASP A:1032 , HOH A:4061BINDING SITE FOR RESIDUE EDO A2455
29DC2SOFTWARETHR A:1073 , LYS A:1107 , THR A:1192 , HOH A:4279BINDING SITE FOR RESIDUE EDO A2456
30DC3SOFTWAREGLY A:521 , GLY A:522 , ASP A:525 , HIS A:799 , HOH A:3321 , HOH A:4531BINDING SITE FOR RESIDUE EDO A2457
31DC4SOFTWARETYR A:889 , ASN A:929 , LEU A:952 , ASN A:968 , HOH A:3976 , HOH A:3979BINDING SITE FOR RESIDUE EDO A2458
32DC5SOFTWARETYR A:563 , LYS A:784 , LYS A:788 , HOH A:4532 , HOH A:4533 , HOH A:4534BINDING SITE FOR RESIDUE EDO A2459
33DC6SOFTWAREASN A:637 , ASP A:641 , PRO A:1049 , HOH A:3523 , HOH A:4038BINDING SITE FOR RESIDUE EDO A2461
34DC7SOFTWARETRP A:1358 , THR A:1359 , ASP A:1360 , SER A:1361 , LYS A:1362 , HOH A:4535BINDING SITE FOR RESIDUE EDO A2462
35DC8SOFTWARETHR A:993 , THR A:994 , TRP A:995BINDING SITE FOR RESIDUE EDO A2463
36DC9SOFTWAREPRO A:322 , ASN A:1388 , ALA A:1389 , HOH A:3008 , HOH A:4536BINDING SITE FOR RESIDUE EDO A2464
37EC1SOFTWARETRP A:724 , TRP A:726 , LYS A:1156 , GLU A:1253 , ASP A:1254 , HOH A:4515BINDING SITE FOR POLY-SACCHARIDE RESIDUES MGC A2433 THROUGH GAL A2434

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A56)

(-) 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 5A56)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A56)

(-) Exons   (0, 0)

(no "Exon" information available for 5A56)

(-) 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:1106
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               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
                5a56 A  316 MEKETGPEVDDSKVTYDTIQSKVLKAVIDQAFPRVKEYSLNGHTLPGQVQQFNQVFINNHRITPEVTYKKINETTAEYLMKLRDDAHLINAEMTVRLQVVDNQLHFDVTKIVNHNQVTPGQKIDDESKLLSSISFLGNALVSVSSDQTGAKFDGATMSNNTHVSGDDHIDVTNPMKDLAKGYMYGFVSTDKLAAGVWSNSQNSYGGGSNDWTRLTAYKETVGNANYVGIHSSEWQWEKAYKGIVFPEYTKELPSAKVVITEDANADKNVDWQDGAIAYRSIMNNPQGWEKVKDITAYRIAMNFGSQAQNPFLMTLDGIKKINLHTDGLGQGVLLKGYGSEGHDSGHLNYADIGKRIGGVEDFKTLIEKAKKYGAHLGIHVNASETYPESKYFNEKILRKNPDGSYSYGWNWLDQGINIDAAYDLAHGRLARWEDLKKKLGDGLDFIYVDVWGNGQSGDNGAWATHVLAKEINKQGWRFAIEWGHGGEYDSTFHHWAADLTYGGYTNKGINSAITRFIRNHQKDAWVGDYRSYGGAANYPLLGGYSMKDFEGWQGRSDYNGYVTNLFAHDVMTKYFQHFTVSKWENGTPVTMTDNGSTYKWTPEMRVELVDADNNKVVVTRKSNDVNSPQYRERTVTLNGRVIQDGSAYLTPWNWDANGKKLSTDKEKMYYFNTQAGATTWTLPSDWAKSKVYLYKLTDQGKTEEQELTVKDGKITLDLLANQPYVLYRSKQTNPEMSWSEGMHIYDQGFNSGTLKHWTISGDASKAEIVKSQGANDMLRIQGNKEKVSLTQKLTGLKPNTKYAVYVGVDNRSNAKASITVNTGEKEVTTYTNKSLALNYVKAYAHNTRRNNATVDDTSYFQNMYAFFTTGADVSNVTLTLSREAGDEATYFDEIRTFENNSSMYGDKHDTGKGTFKQDFENVAQGIFPFVVGGVEGVEDNRTHLSEKHDPYTQRGWNGKKVDDVIEGNWSLKTNGLVSRRNLVYQTIPQNFRFEAGKTYRVTFEYEAGSDNTYAFVVGKGEFQSQASNLEMHELPNTWTDSKKAKKATFLVTGAETGDTWVGIYSTGNASNTRGDSGGNANFRGYNDFMMDNLQIEEITLTGKMLT 1426
                                   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|                                                                                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         1345
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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 5A56)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A56)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A56)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:488 - Pro A:489   [ RasMol ]  
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  5a56
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  GH101_STRPN | Q2MGH6
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 Related Entries

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

UniProtKB/Swiss-Prot
        GH101_STRPN | Q2MGH6: 5a55 5a57 5a58 5a59 5a5a

(-) Related Entries Specified in the PDB File

5a55 THE NATIVE STRUCTURE OF GH101 FROM STREPTOCOCCUS PNEUMONIAE TIGR4
5a57 THE STRUCTURE OF GH101 FROM STREPTOCOCCUS PNEUMONIAE TIGR4 IN COMPLEX WITH PUGT
5a58 THE STRUCTURE OF GH101 D764N MUTANT FROM STREPTOCOCCUS PNEUMONIAE TIGR4 IN COMPLEX WITH SERINYL T-ANTIGEN
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