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(-) Description

Title :  THE STRUCTURE OF GH101 FROM STREPTOCOCCUS PNEUMONIAE TIGR4 IN COMPLEX WITH PUGT
 
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 :  1.46
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
    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, ENDO-ALPHA-GALACTOSAMINIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 30)

Asymmetric/Biological Unit (5, 30)
No.NameCountTypeFull Name
15G01Ligand/Ion(Z)-[(3R,4R,5R,6R)-3-ACETAMIDO-6-(HYDROXYMETHYL)-4,5-BIS(OXIDANYL)OXAN-2-YLIDENE]AMINO]PHENYLCARBAMATE
2CA3Ligand/IonCALCIUM ION
3CIT2Ligand/IonCITRIC ACID
4EDO23Ligand/Ion1,2-ETHANEDIOL
5GAL1Ligand/IonBETA-D-GALACTOSE

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:577 , ASN A:579 , ASP A:581 , ASN A:583 , ASP A:588 , HOH A:3567BINDING SITE FOR RESIDUE CA A2428
02AC2SOFTWAREGLU A:703 , ASP A:728 , HIS A:1258 , HOH A:3760 , HOH A:3892 , HOH A:3893BINDING SITE FOR RESIDUE CA A2429
03AC3SOFTWAREASP A:1233 , GLU A:1235 , GLU A:1281 , TRP A:1284 , ASP A:1411 , HOH A:4762BINDING SITE FOR RESIDUE CA A2430
04AC4SOFTWARESER A:1127 , ASN A:1128 , GLY A:1200 , ASP A:1201 , GLU A:1202 , HOH A:4588 , HOH A:4596 , HOH A:4997 , HOH A:4998BINDING SITE FOR RESIDUE CIT A2431
05AC5SOFTWARETHR A:1162 , ARG A:1163 , ARG A:1164 , HOH A:4660 , HOH A:4669 , HOH A:4670 , HOH A:4677 , HOH A:4784 , HOH A:4999 , HOH A:5000 , HOH A:5001BINDING SITE FOR RESIDUE CIT A2432
06AC6SOFTWARELYS A:635 , PHE A:864 , ASN A:1090 , EDO A:2446 , HOH A:3705 , HOH A:4173 , HOH A:4535 , HOH A:5005BINDING SITE FOR RESIDUE EDO A2434
07AC7SOFTWAREASP A:416 , ASN A:417 , ASP A:1187 , HOH A:4621 , HOH A:5007BINDING SITE FOR RESIDUE EDO A2435
08AC8SOFTWAREASN A:637 , ASP A:641 , GLY A:642 , LYS A:1016 , PRO A:1049 , HOH A:3715 , HOH A:3718 , HOH A:3720 , HOH A:4402BINDING SITE FOR RESIDUE EDO A2436
09AC9SOFTWARESER A:336 , ASP A:416 , GLU A:1139 , GLY A:1185 , HOH A:4619BINDING SITE FOR RESIDUE EDO A2437
10BC1SOFTWAREGLY 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 A2438
11BC2SOFTWARETYR A:563 , LYS A:784 , LYS A:788 , HOH A:4090 , HOH A:5009 , HOH A:5010BINDING SITE FOR RESIDUE EDO A2439
12BC3SOFTWAREGLY A:869 , ARG A:1163 , EDO A:2441 , HOH A:4175 , HOH A:4176 , HOH A:4179 , HOH A:4183 , HOH A:4672 , HOH A:4675 , HOH A:5011BINDING SITE FOR RESIDUE EDO A2440
13BC4SOFTWAREASP A:863 , ARG A:870 , SER A:871 , ASP A:872 , EDO A:2440 , HOH A:4171 , HOH A:4179 , HOH A:4672 , HOH A:4680BINDING SITE FOR RESIDUE EDO A2441
14BC5SOFTWARETHR A:382 , GLU A:392 , HOH A:5012BINDING SITE FOR RESIDUE EDO A2442
15BC6SOFTWARELYS A:607 , HIS A:835 , GLN A:891 , HOH A:5013 , HOH A:5014BINDING SITE FOR RESIDUE EDO A2443
16BC7SOFTWAREGLN A:462 , THR A:463 , ASP A:505 , LYS A:506 , HOH A:3274 , HOH A:5015 , HOH A:5016BINDING SITE FOR RESIDUE EDO A2444
17BC8SOFTWAREGLN A:1096 , HOH A:4516 , HOH A:4519BINDING SITE FOR RESIDUE EDO A2445
18BC9SOFTWARELYS A:635 , TYR A:873 , ASP A:1013 , LYS A:1085 , ALA A:1089 , ASP A:1091 , EDO A:2434 , HOH A:4196BINDING SITE FOR RESIDUE EDO A2446
19CC1SOFTWARETRP A:724 , ASN A:725 , HOH A:3963 , HOH A:5017 , HOH A:5018BINDING SITE FOR RESIDUE EDO A2447
20CC2SOFTWAREVAL A:674 , GLU A:675 , LYS A:678 , HOH A:3794 , HOH A:5020 , HOH A:5021 , HOH A:5022BINDING SITE FOR RESIDUE EDO A2448
21CC3SOFTWAREASN A:374 , HIS A:375 , ARG A:376 , HOH A:3106BINDING SITE FOR RESIDUE EDO A2449
22CC4SOFTWAREHIS A:639 , ASN A:874 , LEU A:1011 , GLN A:1037 , PRO A:1038 , HOH A:5023BINDING SITE FOR RESIDUE EDO A2450
23CC5SOFTWAREPHE A:450 , ASN A:453 , HIS A:545 , SER A:546 , HOH A:3061BINDING SITE FOR RESIDUE EDO A2451
24CC6SOFTWAREASN A:768 , TRP A:797 , HIS A:799 , HOH A:4127 , HOH A:5025BINDING SITE FOR RESIDUE EDO A2452
25CC7SOFTWAREASN A:417 , GLN A:418 , SER A:595 , HOH A:3555 , HOH A:5026BINDING SITE FOR RESIDUE EDO A2453
26CC8SOFTWAREALA A:882 , GLN A:958 , TYR A:963 , THR A:988 , HOH A:4164 , HOH A:4204 , HOH A:4321 , HOH A:4359BINDING SITE FOR RESIDUE EDO A2454
27CC9SOFTWARETYR A:1009 , LYS A:1016 , THR A:1017 , GLN A:1046 , HOH A:4404 , HOH A:4450 , HOH A:5027BINDING SITE FOR RESIDUE EDO A2455
28DC1SOFTWARETYR A:1179 , PHE A:1181 , VAL A:1237 , ALA A:1238 , GLN A:1239 , PHE A:1242 , HOH A:4737BINDING SITE FOR RESIDUE EDO A2456
29DC2SOFTWAREMET A:616 , HIS A:657 , ASP A:658 , GLU A:699 , TRP A:724 , TRP A:726 , ASP A:764 , VAL A:765 , ASN A:768 , GLU A:796 , TRP A:797 , GLN A:868 , ASP A:1254 , HOH A:3642 , HOH A:3728 , HOH A:4059 , HOH A:4065 , HOH A:4611 , HOH A:4663 , HOH A:5002 , HOH A:5004BINDING SITE FOR POLY-SACCHARIDE RESIDUES 5G0 A2433 THROUGH GAL A2457

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A57)

(-) 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 5A57)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A57)

(-) Exons   (0, 0)

(no "Exon" information available for 5A57)

(-) 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...eeeeee..eeeeeee......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..hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5a57 A  316 MEKETGPEVDDSKVTYDTIQSKVLKAVIDQAFPRVKEYSLNGHTLPGQVQQFNQVFINNHRITPEVTYKKINETTAEYLMKLRDDAHLINAEMTVRLQVVDNQLHFDVTKIVNHNQVTPGQKIDDESKLLSSISFLGNALVSVSSDQTGAKFDGATMSNNTHVSGDDHIDVTNPMKDLAKGYMYGFVSTDKLAAGVWSNSQNSYGGGSNDWTRLTAYKETVGNANYVGIHSSEWQWEKAYKGIVFPEYTKELPSAKVVITEDANADKNVDWQDGAIAYRSIMNNPQGWEKVKDITAYRIAMNFGSQAQNPFLMTLDGIKKINLHTDGLGQGVLLKGYGSEGHDSGHLNYADIGKRIGGVEDFKTLIEKAKKYGAHLGIHVNASETYPESKYFNEKILRKNPDGSYSYGWNWLDQGINIDAAYDLAHGRLARWEDLKKKLGDGLDFIYVDVWGNGQSGDNGAWATHVLAKEINKQGWRFAIEWGHGGEYDSTFHHWAADLTYGGYTNKGINSAITRFIRNHQKDAWVGDYRSYGGAANYPLLGGYSMKDFEGWQGRSDYNGYVTNLFAHDVMTKYFQHFTVSKWENGTPVTMTDNGSTYKWTPEMRVELVDADNNKVVVTRKSNDVNSPQYRERTVTLNGRVIQDGSAYLTPWNWDANGKKLSTDKEKMYYFNTQAGATTWTLPSDWAKSKVYLYKLTDQGKTEEQELTVKDGKITLDLLANQPYVLYRSKQTNPEMSWSEGMHIYDQGFNSGTLKHWTISGDASKAEIVKSQGANDMLRIQGNKEKVSLTQKLTGLKPNTKYAVYVGVDNRSNAKASITVNTGEKEVTTYTNKSLALNYVKAYAHNTRRNNATVDDTSYFQNMYAFFTTGADVSNVTLTLSREAGDEATYFDEIRTFENNSSMYGDKHDTGKGTFKQDFENVAQGIFPFVVGGVEGVEDNRTHLSEKHDPYTQRGWNGKKVDDVIEGNWSLKTNGLVSRRNLVYQTIPQNFRFEAGKTYRVTFEYEAGSDNTYAFVVGKGEFQSQASNLEMHELPNTWTDSKKAKKATFLVTGAETGDTWVGIYSTGNASNTRGDSGGNANFRGYNDFMMDNLQIEEITLTGKMLTE 1427
                                   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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  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 5A57)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A57)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A57)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  5a57
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 Related Entries

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

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        GH101_STRPN | Q2MGH6: 5a55 5a56 5a58 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
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