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(-) Description

Title :  CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE TYPE 1 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 :  11 Nov 14  (Deposition) - 26 Nov 14  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
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, 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, 10)

Asymmetric/Biological Unit (6, 10)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3FUC1Ligand/IonALPHA-L-FUCOSE
4GAL1Ligand/IonBETA-D-GALACTOSE
5NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO44Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:451 , HIS A:496 , GLU A:500 , HOH A:3057BINDING SITE FOR RESIDUE EDO A 2012
2AC2SOFTWAREPRO A:467 , LYS A:731 , ARG A:735BINDING SITE FOR RESIDUE SO4 A 2013
3AC3SOFTWAREARG A:486 , ARG A:776 , GLU A:777 , GLN A:778BINDING SITE FOR RESIDUE SO4 A 2014
4AC4SOFTWAREGLN A:448 , SER A:823 , THR A:824 , HOH A:3581 , HOH A:3582 , HOH A:3583BINDING SITE FOR RESIDUE SO4 A 2015
5AC5SOFTWARELYS A:747 , ASP A:849 , SER A:892 , HOH A:3503 , HOH A:3662 , HOH A:3665 , HOH A:3818BINDING SITE FOR RESIDUE SO4 A 2016
6AC6SOFTWAREGLY A:631 , ASP A:633 , SER A:634 , GLY A:766 , THR A:774 , ARG A:776 , GLU A:777 , THR A:779BINDING SITE FOR RESIDUE EDO A 2017
7AC7SOFTWARETYR A:440 , HIS A:479 , ASP A:481 , THR A:523 , 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:3105 , HOH A:3184 , HOH A:3422 , HOH A:3809 , HOH A:3810 , HOH A:3811 , HOH A:3812 , HOH A:3813 , HOH A:3815 , HOH A:3816Binding site for Poly-Saccharide residues FUC A2008 through A2G A2011

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D6H)

(-) 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 4D6H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D6H)

(-) Exons   (0, 0)

(no "Exon" information available for 4D6H)

(-) 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:587
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               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..............hhhhhhhhhhhhhhhhhhhhhhh....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
                4d6h A  421 EVDKRREINNEHPLLMMPLYANGEEFNQGKYTFWGGDTLTGKWENIPDDLKPYTVIQLHPDDLPKRDGAARDFYEHMLEEAAKYVNPKTGKNEPIPVILTVYTAGNMPYYTSAHWLSTSWIDKMYQKYPNLHGIFSTASYWIWANDIENKAADYLKVSAKNGGYFIWAEQNSGSAIEKAFGKNGKIAFQKSVDKYWKNLIFMFKNTPAAEGNDSTTESYMKGLWLSNHTYQWGGLMDTWKWYETGKWKLFASGNIGKSQGDRQWLTEPESMLGEEALGVYLNGGVVYNFEHPAYTYGVNNKESLLFSEVIKEFFRYVIAHPAPSKEKVLEDTKVFIHGDYSNKGNGKFFVNVNTDREQTPLYMTGRYNVIPAIPGVLKTDKLKESVSSSRIQIKEITSPEFSSTQARKEYLNKLYPMNYEGDIFAQKLDNRWFVYNYKVNENVKQTGKLKFNSLEMNVEFEPHTYGIFERISNGLKVNLNNFRTNKDSLWSNAQDANQAKKLPQLTKKGAIKWIEEHYIKDTQFGEKRVTKIVLRGIDKLPTIHSLSGTNNSYDQPSLNFDQKNHMVTITINSNGNLEFELHFLEHT 1007
                                   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 4D6H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D6H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D6H)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4D6H)

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

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 Related Entries

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(-) Related Entries Specified in the PDB File

4d6c CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98)
4d6d CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TRISACCHARIDE
4d6e CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TRISACCHARIDE
4d6f CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TETRASACCHARIDE (E558A, X01 MUTANT)
4d6g CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE BLOOD GROUP A-TRISACCHARIDE (L19 MUTANT)
4d6i CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE TYPE 1 BLOOD GROUP A- TETRASACCHARIDE (E558A L19 MUTANT)
4d6j CRYSTAL STRUCTURE OF A FAMILY 98 GLYCOSIDE HYDROLASE CATALYTIC MODULE (SP3GH98) IN COMPLEX WITH THE TYPE 2 BLOOD GROUP A- TETRASACCHARIDE (E558A X01 MUTANT)