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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALPHA-L-IDURONIDASE COMPLEX WITH 5-FLUORO-ALPHA-L-IDOPYRANOSYLURONIC ACID FLUORIDE
 
Authors :  H. Bie, J. Yin, X. He, A. R. Kermode, E. D. Goddard-Borger, S. G. Withers, M. N. G. James
Date :  29 Apr 13  (Deposition) - 18 Sep 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycoside Hydrolase Family 39, Tim Barrel, Beta Sandwich, Fibronectin Iii Domain, Glycosaminoglycans, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Bie, J. Yin, X. He, A. R. Kermode, E. D. Goddard-Borger, S. G. Withers M. N. James
Insights Into Mucopolysaccharidosis I From The Structure An Action Of Alpha-L-Iduronidase.
Nat. Chem. Biol. V. 9 739 2013
PubMed-ID: 24036510  |  Reference-DOI: 10.1038/NCHEMBIO.1357

(-) Compounds

Molecule 1 - ALPHA-L-IDURONIDASE
    ChainsA, B
    EC Number3.2.1.76
    EngineeredYES
    Expression SystemARABIDOPSIS THALIANA
    Expression System CommonTHALE CRESS
    Expression System PlasmidPARC5S3
    Expression System StrainCGL1 1
    Expression System Taxid3702
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 27-653
    GeneIDUA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 32)

Asymmetric Unit (7, 32)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CL1Ligand/IonCHLORIDE ION
3GOL7Ligand/IonGLYCEROL
4IDF2Ligand/Ion5-FLUORO-ALPHA-L-IDOPYRANOSYLURONIC ACID FLUORIDE
5MAN8Ligand/IonALPHA-D-MANNOSE
6NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
7TLA2Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (5, 11)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CL-1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4IDF1Ligand/Ion5-FLUORO-ALPHA-L-IDOPYRANOSYLURONIC ACID FLUORIDE
5MAN2Ligand/IonALPHA-D-MANNOSE
6NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
7TLA-1Ligand/IonL(+)-TARTARIC ACID
Biological Unit 2 (6, 20)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CL-1Ligand/IonCHLORIDE ION
3GOL5Ligand/IonGLYCEROL
4IDF1Ligand/Ion5-FLUORO-ALPHA-L-IDOPYRANOSYLURONIC ACID FLUORIDE
5MAN6Ligand/IonALPHA-D-MANNOSE
6NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
7TLA2Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:324 , ASN A:415 , HIS A:416 , ASP A:444 , ASP A:445 , ARG A:447BINDING SITE FOR RESIDUE GOL A 909
02AC2SOFTWAREHIS A:356 , PRO A:359 , ARG A:368 , PHE A:369 , GLN A:370 , VAL A:494BINDING SITE FOR RESIDUE GOL A 910
03AC3SOFTWAREHIS A:91 , ASN A:181 , GLU A:182 , LYS A:264 , GLU A:299 , VAL A:304 , GLY A:305 , TRP A:306 , ASP A:349 , ARG A:363BINDING SITE FOR RESIDUE IDF A 911
04AC4SOFTWAREHIS B:356 , ARG B:368 , PHE B:369 , GLN B:370 , VAL B:494 , NAG B:904BINDING SITE FOR RESIDUE GOL B 913
05AC5SOFTWARELEU B:40 , TRP B:41 , ASN B:331 , GLN B:400 , ALA B:403BINDING SITE FOR RESIDUE GOL B 914
06AC6SOFTWAREARG A:210 , ALA A:211 , PRO B:594BINDING SITE FOR RESIDUE GOL B 915
07AC7SOFTWAREARG B:100 , TYR B:109 , ASN B:110 , PHE B:111 , ARG B:162 , NAG B:901BINDING SITE FOR RESIDUE GOL B 916
08AC8SOFTWAREGLN B:71 , ALA B:75 , LEU B:120 , GLU B:123 , ASN B:124 , ARG B:555BINDING SITE FOR RESIDUE GOL B 917
09AC9SOFTWAREARG B:44 , ARG B:45 , ARG B:48BINDING SITE FOR RESIDUE TLA B 918
10BC1SOFTWAREARG B:48 , ARG B:83 , LYS B:86 , LYS B:174 , PRO B:467 , GLY B:468BINDING SITE FOR RESIDUE TLA B 919
11BC2SOFTWAREHIS B:91 , ASN B:181 , GLU B:182 , LYS B:264 , GLU B:299 , VAL B:304 , GLY B:305 , TRP B:306 , ASP B:349 , PHE B:352 , ARG B:363 , MAN B:910BINDING SITE FOR RESIDUE IDF B 920
12BC3SOFTWAREPRO B:302 , LEU B:303 , ARG B:313 , ARG B:363BINDING SITE FOR RESIDUE CL B 921
13BC4SOFTWAREASN A:110 , THR A:112 , HIS A:113BINDING SITE FOR MONO-SACCHARIDE NAG A 901 BOUND TO ASN A 110
14BC5SOFTWARETYR A:355 , HIS A:356 , GLN A:370 , ASN A:372 , VAL A:494 , PHE A:495BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 372 RESIDUES 904 TO 908
15BC6SOFTWAREGLU A:274 , ASN A:415BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 415 RESIDUES 902 TO 903
16BC7SOFTWAREARG B:100 , ASN B:110 , THR B:112 , HIS B:113 , GOL B:916BINDING SITE FOR MONO-SACCHARIDE NAG B 901 BOUND TO ASN B 110
17BC8SOFTWAREPRO A:357 , LEU A:490 , GLY A:491 , ARG A:492 , PRO A:493 , VAL A:494 , PHE A:495 , CYS B:53 , PRO B:54 , LEU B:56 , TRP B:306 , SER B:307 , PRO B:309 , PHE B:352 , TYR B:355 , HIS B:356 , GLN B:370 , ASN B:372 , VAL B:494 , PHE B:495 , GOL B:913 , IDF B:920BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 372 RESIDUES 904 TO 912
18BC9SOFTWAREGLU B:274 , ASN B:415BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 415 RESIDUES 902 TO 903

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:541 -A:577
2B:541 -B:577

(-) Cis Peptide Bonds  (11, 11)

Asymmetric 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
6His B:186 -Asp B:187
7Gly B:220 -Pro B:221
8Pro B:228 -Pro B:229
9His B:356 -Pro B:357
10Arg B:375 -Pro B:376
11Leu B:532 -Pro B:533

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KGJ)

(-) Sequences/Alignments

Asymmetric 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:595
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee......eeee......hhhhhhhhhhhhh.......eeee.hhhhh.......hhhhhhhhhhhhhh..eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee...hhhhh.......hhhhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhh.............eeee......hhhhhhhhhhhhhhhhhhhhhhhh...eee............hhhhhhhhhhhhhhhhhhhhhhhhh........eeee...................eeeeee......eeeeeehhhhhhhhhhh....eeeeeeeee..eee.....eeeeeeee.........eeeeeeee......eeeeeeeeeeeee........eeeeeeee....hhhhhhhhh......hhhhhhhhhhh...ee...ee......eee..eeee.eeeeeeee..........eeeeeeeee..eeeeeee........eeeeeeeee...ee.........eeee........eeeeeeeee...........eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgj A  28 APHLVQVDAARALWPLRRFWRSTGFCPPYVLSWDQQLNLAYVGAVPHRGIKQVRTHWLLELVTTLSYNFTHLDGYLDLLRENQLLPGFELMGSASGHFTDFEDKQQVFEWKDLVSSLARRYIGRYGLAHVSKWNFETWNEPDHHDFDNVSMTMQGFLNYYDACSEGLRAASPALRLGGPGDSFHTPPRSPLSWGLLRHCHDGTNFFTGEAGVRLDYISLHRKGARSSISILEQEKVVAQQIRQLFPKFADTPIYNDEADPLVGWSLPQPWRADVTYAAMVVKVIAQHQNLLLANTTSAFPYALLSNDNAFLSYHPHPFAQRTLTARFQVNNTRPPHVQLLRKPVLTAMGLLALLDEEQLWAEVSQAGTVLDSNHTVGVLASAHRPQGPADAWRAAVLIYASDDTRAHPNRSVAVTLRLRGVPPGPGLVYVTRYLDNGLCSPDGEWRRLGRPVFPTAEQFRRMRAAEDPVAAAPRPLPAGGRLTLRPALRLPSLLLVHVCARPEKPPGQVTRLRALPLTQGQLVLVWSDEHVGSKCLWTYEIQFSQDYTPVSRKPSTFNLFVFSPDTGAVSGSYRVRALDYWARPGPFSDPVPYLE 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       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582     ||595       605       615       625       635     
                                                      55|                                 99|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              588|                                                
                                                       64                                 107                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               592                                                

Chain B from PDB  Type:PROTEIN  Length:607
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee......eeee.....hhhhhhhhhhhhhhhhh.......eeee.hhhhh.eee....eeehhhhhhhhhhhhhh..eeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee...hhhhh.......hhhhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhh..............eeee......hhhhhhhhhhhhhhhhhhhhhhhh...eee............hhhhhhhhhhhhhhhhhhhhhhh..........eeee...................eeeeee......eeeeeehhhhhhhhhhhh...eeeeeeeee..ee......eeeeeeee.........eeeeeeee...........eeeeeeee........eeeeeeee....hhhhhhhhh......hhhhhhhhhh....ee...ee......eee..ee...eeeeeeee..........eeeeeeeee..eeeeeee........eeeeeeeeehhhh..ee.........eeee........eeeeeeeee...........eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kgj B  28 APHLVQVDAARALWPLRRFWRSTGFCPPLDPYVLSWDQQLNLAYVGAVPHRGIKQVRTHWLLELVTTRGSTLSYNFTHLDGYLDLLRENQLLPGFELMGSASGHFTDFEDKQQVFEWKDLVSSLARRYIGRYGLAHVSKWNFETWNEPDHHDFDNVSMTMQGFLNYYDACSEGLRAASPALRLGGPGDSFHTPPRSPLSWGLLRHCHDGTNFFTGEAGVRLDYISLHRKGARSSISILEQEKVVAQQIRQLFPKFADTPIYNDEADPLVGWSLPQPWRADVTYAAMVVKVIAQHQNLLLANTTSAFPYALLSNDNAFLSYHPHPFAQRTLTARFQVNNTRPPHVQLLRKPVLTAMGLLALLDEEQLWAEVSQAGTVLDSNHTVGVLASAHRPQGPADAWRAAVLIYASDDTRAHPNRSVAVTLRLRGVPPGPGLVYVTRYLDNGLCSPDGEWRRLGRPVFPTAEQFRRMRAAEDPVAAAPRPLPAGGRLTLRPALRLPSLLLVHVCARPEKPPGQVTRLRALPLTQGQLVLVWSDEHVGSKCLWTYEIQFSQDGKAYTPVSRKPSTFNLFVFSPDTGAVSGSYRVRALDYWARPGPFSDPVPYLEVP 642
                                    37        47        62        72        82        92       102||     115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       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       
                                                       56|                                      103|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                                        62                                       107                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       

   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 4KGJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        IDUA_HUMAN | P354751y24 3w81 3w82 4kgl 4kh2 4mj2 4mj4 4obr 4obs

(-) Related Entries Specified in the PDB File

4jxo 4jxp 4kgl 4kh2