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(-) Description

Title :  THE NATIVE STRUCTURE OF GH101 FROM STREPTOCOCCUS PNEUMONIAE TIGR4
 
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 :  1.85
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  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:577 , ASN A:579 , ASP A:581 , ASN A:583 , ASP A:588 , HOH A:3479BINDING SITE FOR RESIDUE CA A2419
2AC2SOFTWAREGLU A:703 , ASP A:728 , HIS A:1258 , HOH A:3633 , HOH A:3740 , HOH A:3741BINDING SITE FOR RESIDUE MN A2420
3AC3SOFTWAREASP A:1233 , GLU A:1235 , GLU A:1281 , TRP A:1284 , ASP A:1411 , HOH A:4454BINDING SITE FOR RESIDUE CA A2421
4AC4SOFTWAREGLY A:1063 , ASN A:1090 , ASP A:1091 , ASP A:1207 , HOH A:4222 , HOH A:4223BINDING SITE FOR RESIDUE CA A2422
5AC5SOFTWARESER A:1127 , ASN A:1128 , ASP A:1201 , GLU A:1202 , HOH A:4317BINDING SITE FOR RESIDUE EDO A2423
6AC6SOFTWARESER A:314 , HIS A:315 , HOH A:3002 , HOH A:3003 , HOH A:4542BINDING SITE FOR RESIDUE CA A2425
7AC7SOFTWARETYR A:816 , GLN A:868BINDING SITE FOR RESIDUE EDO A2424

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A55)

(-) 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 5A55)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A55)

(-) Exons   (0, 0)

(no "Exon" information available for 5A55)

(-) 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:1100
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               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........hhhhhhhhhhhhhhhhh..eeeeeee.....................hhhhhhhhhhhhhh...eeeeeeee..ee.......hhhh..........eeee...eeee.hhhhhhhhhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhhh..eeee.........eeeehhhhh............hhhhhhhhhhhh......hhhhhhhhh..............hhhh.hhhhhhhhhhhhhhhhhhhhh.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 Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5a55 A  314 SHMEKETGPEVDDSKVTYDTIQSKVLKAVIDQAFPRVKEYSLNGHTLPGQVQQFNQVFINNHRITPEVTYKKINETTAEYLMKLRDDAHLINAEMTVRLQVVDNQLHFDVTKIVNHNQVTPGQKIDDESKLLSSISFLGNALVSVSSDQTGAKFDGATMSNNTHVSGDDHIDVTNPMKDLAKGYMYGFVSTDKLAAGVWSNSQNSYGGGSNDWTRLTAYKETVGNANYVGIHSSEWQWEKAYKGIVFPEYTKELPSAKVVITEDANADKNVDWQDGAIAYRSIMNNPQGWEKVKDITAYRIAMNFGSQAQNPFLMTLDGIKKINLHTDGLGQGVLLKGYGSEGHDSGHLNYADIGKRIGGVEDFKTLIEKAKKYGAHLGIHVNASETYPESKYFNEKILRKNPDGSYSYGWNWLDQGINIDAAYDLAHGRLARWEDLKKKLGDGLDFIYVDVWGNGQSGDNGAWATHVLAKEINKQGWRFAIEWGHGGEYDSTFHHWAADLTYGGYTNKGINSAITRFIRNHQKDAWVGDYRSYGGAANYPLLGGYSMKDFEGWQGRSDYNGYVTNLFAHDVMTKYFQHFTVSKWENGTPVTMTDNGSTYKWTPEMRVELVDADNNKVVVTRKSNDVNSPQYRERTVTLNGRVIQDGSAYLTPWNWDANGKKLSTDKEKMYYFNTQAGATTWTLPSDWAKSKVYLYKLTDQGKTEEQELTVKDGKITLDLLANQPYVLYRSKQTNPEMSWSEGMHIYDQGFNSGTLKHWTISGDASKAEIVKSQGANDMLRIQGNKEKVSLTQKLTGLKPNTKYAVYVGVDNRSNAKASITVNTGEKEVTTYTNKSLALNYVKAYAHNTRRNNATVDDTSYFQNMYAFFTTGADVSNVTLTLSREAGDEATYFDEIRTFENNSSMYGDKHDTGKGTFKQDFENVAQGIFPFVVGGVEGVEDNRTHLSEKHDPYTQRGWNGKKVDDVIEGNWSLKTNGLVSRRNLVYQTIPQNFRFEAGKTYRVTFEYEAGSDNTYAFVVGKGEFQSQASNLEMHELPNTWTDSKKAKKATFLVTGAETGDTWVGIYSTGNASNTRGDSGGNANFRGYNDFMMDNLQIEEI 1418
                                   323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333     |1348      1358      1368      1378      1388      1398      1408      1418
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          1339|                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           1345
   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 5A55)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A55)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A55)

(-) 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 ]  
    Asp A:1264 - Pro A:1265   [ RasMol ]  
    Phe A:1242 - Pro A:1243   [ RasMol ]  
 

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  5a55
    Family and Domain Information: ProDom | SYSTERS
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  GH101_STRPN | Q2MGH6
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  3.2.1.97
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 Related Entries

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

UniProtKB/Swiss-Prot
        GH101_STRPN | Q2MGH6: 5a56 5a57 5a58 5a59 5a5a

(-) Related Entries Specified in the PDB File

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
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