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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALPHA-L-IDURONIDASE IN THE P212121 FORM
 
Authors :  H. Bie, J. Yin, X. He, A. R. Kermode, M. N. G. James
Date :  07 Jan 14  (Deposition) - 14 Jan 15  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycoside Hydrolase Family 39, Tim Barrel, Beta Sandwich, Fibronectin Iii Domain, Glycosaminoglycans, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Bie, J. Yin, X. He, A. R. Kermode, M. N. G. James
Crystal Structure Of Human Alpha-L-Iduronidase In The P212121 Form
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALPHA-L-IDURONIDASE
    Chains: A
    EC Number: 3.2.1.76
    Engineered: YES
    Expression System: ARABIDOPSIS THALIANA
    Expression System Common: THALE CRESS
    Expression System Plasmid: PARC5S3
    Expression System Strain: CGL1 1
    Expression System Taxid: 3702
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 27-653
    Gene: IDUA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 16)

Asymmetric/Biological Unit (6, 16)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CL1Ligand/IonCHLORIDE ION
3GOL6Ligand/IonGLYCEROL
4MAN3Ligand/IonALPHA-D-MANNOSE
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO41Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:41 , ALA A:335 , LEU A:401 , TRP A:402 , ALA A:403 , HOH A:1097 , HOH A:1113BINDING SITE FOR RESIDUE GOL A 909
02AC2SOFTWAREGLN A:71 , ALA A:75 , LEU A:120 , GLU A:123 , ASN A:124 , ARG A:555BINDING SITE FOR RESIDUE GOL A 910
03AC3SOFTWAREGLN A:147 , PHE A:150 , THR A:552 , ARG A:553 , LEU A:554 , HOH A:1052BINDING SITE FOR RESIDUE GOL A 911
04AC4SOFTWAREVAL A:494 , PHE A:495 , ALA A:627 , HOH A:1110BINDING SITE FOR RESIDUE GOL A 912
05AC5SOFTWARELYS A:324 , HIS A:416 , ASP A:444 , ASP A:445 , HOH A:1071BINDING SITE FOR RESIDUE GOL A 913
06AC6SOFTWAREPRO A:357 , GLU A:582 , SER A:596 , ARG A:597 , HOH A:1112 , HOH A:1119BINDING SITE FOR RESIDUE GOL A 914
07AC7SOFTWAREPRO A:302 , LEU A:303 , TRP A:312 , ARG A:313 , ARG A:363BINDING SITE FOR RESIDUE CL A 915
08AC8SOFTWAREARG A:48 , ARG A:83 , LYS A:86BINDING SITE FOR RESIDUE SO4 A 916
09AC9SOFTWAREASN A:110 , THR A:112 , HIS A:113BINDING SITE FOR MONO-SACCHARIDE NAG A 901 BOUND TO ASN A 110
10BC1SOFTWARESER A:307 , PRO A:309 , TYR A:355 , HIS A:356 , GLN A:370 , ASN A:372 , VAL A:494 , PHE A:495 , SER A:596 , ARG A:597 , LYS A:598 , HOH A:1067BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 372 RESIDUES 903 TO 908
11BC2SOFTWAREGLU A:274 , ASN A:415BINDING SITE FOR MONO-SACCHARIDE NAG A 902 BOUND TO ASN A 415

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:541 -A:577

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly A:220 -Pro A:221
2Pro A:228 -Pro A:229
3His A:356 -Pro A:357
4Arg A:375 -Pro A:376
5Leu A:532 -Pro A:533

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OBS)

(-) 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:594
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee......eeee..hhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhh.......hhhhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhh.......hhhhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhh.............eeee......hhhhhhhhhhhhhhhhhhhhhhhh...eee............hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.................eeeeee......eeeeeehhhhhhhhhhhh...eeeeeeeee..eee.....eeeeeeee.........eeeeeeee......eeeeeeeeeeeee........eeeeeeee....hhhhhhhhh......hhhhhhhhhh....ee...ee......eee..eeee.eeeeeeee..........eeeeeeeee..eeeeeee........eeeeeeeee......ee.........eeee........eeeeeeeee...........eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4obs A  28 APHLVQVDAARALWPLRRFWRSTGFCPPYVLSWDQQLNLAYVGAVPHRGIKQVRTHWLLELVTTLSYNFTHLDGYLDLLRENQLLPGFELMGSASGHFTDFEDKQQVFEWKDLVSSLARRYIGRYGLAHVSKWNFETWNEPDHHDFDNVSMTMQGFLNYYDACSEGLRAASPALRLGGPGDSFHTPPRSPLSWGLLRHCHDGTNFFTGEAGVRLDYISLHRKGARSSISILEQEKVVAQQIRQLFPKFADTPIYNDEADPLVGWSLPQPWRADVTYAAMVVKVIAQHQNLLLAAFPYALLSNDNAFLSYHPHPFAQRTLTARFQVNNTRPPHVQLLRKPVLTAMGLLALLDEEQLWAEVSQAGTVLDSNHTVGVLASAHRPQGPADAWRAAVLIYASDDTRAHPNRSVAVTLRLRGVPPGPGLVYVTRYLDNGLCSPDGEWRRLGRPVFPTAEQFRRMRAAEDPVAAAPRPLPAGGRLTLRPALRLPSLLLVHVCARPEKPPGQVTRLRALPLTQGQLVLVWSDEHVGSKCLWTYEIQFSQDGKAYTPVSRKPSTFNLFVFSPDTGAVSGSYRVRALDYWARPGPFSDPVPYLE 640
                                    37        47      ||65        75        85        95   ||  112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332  ||   346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636    
                                                     54|                                  99|                                                                                                                                                                                                                                 335|                                                                                                                                                                                                                                                                                                            
                                                      63                                  107                                                                                                                                                                                                                                  340
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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 4OBS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Leu A:532 - Pro A:533   [ RasMol ]  
    Pro A:228 - Pro A:229   [ RasMol ]  
 

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  IDUA_HUMAN | P35475
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  3.2.1.76
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 Related Entries

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

UniProtKB/Swiss-Prot
        IDUA_HUMAN | P35475: 1y24 3w81 3w82 4kgj 4kgl 4kh2 4mj2 4mj4 4obr

(-) Related Entries Specified in the PDB File

4kgj IDURONIDASE COMPLEX WITH 5-FLUORO-ALPHA-L- IDOPYRANOSYLURONIC ACID FLUORIDE
4kgl IDURONIDASE COMPLEX WITH [2R,3R,4R,5S]-2-CARBOXY-3,4,5- TRIHYDROXY-PIPERIDINE
4kh2 IDURONIDASE COMPLEX WITH 2-DEOXY-2-FLUORO-ALPHA-L- IDOPYRANOSYLURONIC ACID FLUORIDE
4mj2 R3 APO-IDUA STRUCTURE
4mj4 P21 APO-IDURONIDASE STRUCTURE
4obr