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(-) Description

Title :  CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE TYPE 2 BLOOD GROUP A-TETRASACCHARIDE (E558A X02 MUTANT)
 
Authors :  D. H. Kwan, I. Constantinescu, R. Chapanian, M. A. Higgins, E. Samain, A. B. Boraston, J. N. Kizhakkedathu, S. G. Withers
Date :  19 Nov 14  (Deposition) - 21 Jan 15  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Blood Group Antigen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Kwan, I. Constantinescu, R. Chapanian, M. A. Higgins, M. Koetzler, E. Samain, A. B. Boraston, J. N. Kizhakkedathu, S. G. Withers
Towards Efficient Enzymes For The Generation Of Universal Blood Through Structure-Guided Directed Evolution.
J. Am. Chem. Soc. V. 137 5695 2015
PubMed-ID: 25870881  |  Reference-DOI: 10.1021/JA5116088

(-) Compounds

Molecule 1 - GLYCOSIDE HYDROLASE
    Chains: A
    EC Number: 3.2.1.102
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET29
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 423-1005
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 406556
    Strain: SP3-BS71

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric/Biological Unit (6, 9)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3FUC1Ligand/IonALPHA-L-FUCOSE
4GAL1Ligand/IonBETA-D-GALACTOSE
5NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:631 , ASP A:633 , SER A:634 , GLY A:766 , VAL A:770 , THR A:774 , ARG A:776 , GLU A:777 , THR A:779BINDING SITE FOR RESIDUE EDO A 2011
2AC2SOFTWAREARG A:486 , ARG A:776 , GLU A:777 , GLN A:778BINDING SITE FOR RESIDUE SO4 A 2012
3AC3SOFTWAREPRO A:467 , LYS A:731 , ARG A:735BINDING SITE FOR RESIDUE SO4 A 2013
4AC4SOFTWAREARG A:786 , ASN A:832 , MET A:837 , HOH A:3567BINDING SITE FOR RESIDUE SO4 A 2014
5AC5SOFTWARELYS A:747 , ASP A:849 , SER A:892 , HOH A:3486 , HOH A:3628 , HOH A:3779BINDING SITE FOR RESIDUE SO4 A 2015
6AC6SOFTWARETYR A:440 , HIS A:479 , ASP A:481 , THR A:523 , TYR A:530 , THR A:557 , TYR A:560 , TRP A:561 , THR A:626 , TRP A:659 , TYR A:662 , GLU A:663 , GLU A:710 , HIS A:711 , PRO A:712 , LYS A:927 , HOH A:3100 , HOH A:3188 , HOH A:3191 , HOH A:3318 , HOH A:3371 , HOH A:3372 , HOH A:3411 , HOH A:3435 , HOH A:3768 , HOH A:3769 , HOH A:3770 , HOH A:3771 , HOH A:3772 , HOH A:3773 , HOH A:3774 , HOH A:3775 , HOH A:3776 , HOH A:3777Binding site for Poly-Saccharide residues FUC A2007 through A2G A2010

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D71)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:710 -His A:711

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D71)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D71)

(-) Exons   (0, 0)

(no "Exon" information available for 4D71)

(-) 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:586
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee.hhhhhhh.........hhhhhhhhh...hhh.eeeeee........hhhhhhhhhhhhhhhhh............eeeeeee.hhh...hhhhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhh.....hhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhh..............hhhhhh...hhhhhhhhhhhhhh....eeeeehhhhhhee..eehhhhhhhhhhhhhhhhhh...hhhhhhhhh.eeee.hhhhhhhhhhhh.....................ee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhh........eeeee..eeeee.........eeeeeee..eeeeeee....eeeeeee..eeeeeee.....hhhhhh...hhhhhhh....hhhhhhhhhhhhh.........eeeeeeee......eeeeeee........eeeee....eeeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4d71 A  421 EVDKRREINNEHPLLMMPLYANGEEFNQGKYTFWGGDTLTGKWENIPDDLKPYTVIQLHPDDLPKRDGAARDFYEHMLEEAAKYVNPKTGKNEPIPVILTVYTAGNMPYYTSAHWLSTSWIDKMYQKYPNLHGIFSTASYWIWANDIENKAADYLKVSAKNGGYFIWAEQNSGSAIEKAFGKNGKIAFQKSVDKYWKNLIFMFKNTPAAEGNDSTTESYMKGLWLSNHTYQWGGLMDTWKWYETGKWKLFASGNIGKSQGDRQWLTEPESMLGEEALGVYLNGGVVYNFEHPAYTYGVNNKESLLFSEVIKEFFRYVIAHPAPSKEKVLEDTKVFIHGDYSNKGNGKFFVNVNTDREQTPLYMTGRYNVIPAIPGVLKTDKLKESVSSSRIQIKEITSPEFSSTQARKEYLNKLYPMNYEGDIFAQKLDNRWFVYNYKVNENVKQTGKLKFNSLEMNVEFEPHTYGIFERISNGLKVNLNNFRTNKDSLWSNAQDANQAKKLPQLTKKGAIKWIEEHYIKDTQFGEKRVTKIVLRGIDKLPTIHSLSGTNNSYDQPSLNFDQKNHMVTITINSNGNLEFELHFLEH 1006
                                   430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000
   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 4D71)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D71)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D71)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4D71)

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  Cis Peptide Bonds
    Glu A:710 - His A:711   [ RasMol ]  
 

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4d72 CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE TYPE 2 BLOOD GROUP A- TETRASACCHARIDE (E558A L19 MUTANT)