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(-) Description

Title :  CRYSTAL STRUCTURE OF APO-IDURONIDASE IN THE R3 FORM
 
Authors :  H. Bie, J. Yin, X. He, A. R. Kermode, E. D. Goddard-Borger, S. G. Withers, M. N. G. James
Date :  03 Sep 13  (Deposition) - 18 Sep 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tim Barrel, Beta Sandwich, Fibronectin Type Iii, Hydrolyze Iduronic Acids From The Non-Reducing Ends Of Glycosaminoglycan, Intracellular, Lysosomal, Hydrolase (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
    Chains: A, B
    EC Number: 3.2.1.76
    Engineered: YES
    Expression System: ARABIDOPSIS THALIANA
    Expression System Common: THALE CRESS
    Expression System Strain: CGL CS6192
    Expression System Taxid: 3702
    Gene: IDUA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 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, 30)

Asymmetric Unit (7, 30)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2CL2Ligand/IonCHLORIDE ION
3GOL6Ligand/IonGLYCEROL
4MAN6Ligand/IonALPHA-D-MANNOSE
5NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SRT1Ligand/IonS,R MESO-TARTARIC ACID
7TLA2Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (4, 9)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4MAN2Ligand/IonALPHA-D-MANNOSE
5NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SRT-1Ligand/IonS,R MESO-TARTARIC ACID
7TLA-1Ligand/IonL(+)-TARTARIC ACID
Biological Unit 2 (6, 19)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CL-1Ligand/IonCHLORIDE ION
3GOL5Ligand/IonGLYCEROL
4MAN4Ligand/IonALPHA-D-MANNOSE
5NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SRT1Ligand/IonS,R MESO-TARTARIC ACID
7TLA2Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:324 , HIS A:416 , THR A:417 , ASP A:444 , ASP A:445 , ARG A:447 , HOH A:1150BINDING SITE FOR RESIDUE GOL A 909
02AC2SOFTWAREPRO A:302 , LEU A:303 , ARG A:313 , ARG A:363BINDING SITE FOR RESIDUE CL A 910
03AC3SOFTWARETHR B:388 , GLY B:391 , ASP B:509 , SER B:600 , THR B:601 , PHE B:602 , HOH B:1046 , HOH B:1228 , HOH B:1236BINDING SITE FOR RESIDUE GOL B 912
04AC4SOFTWAREHIS B:356 , ARG B:368 , PHE B:369 , GLN B:370 , VAL B:494 , PHE B:495 , NAG B:905 , HOH B:1057 , HOH B:1058BINDING SITE FOR RESIDUE GOL B 913
05AC5SOFTWARETRP B:41 , ASN B:331 , LEU B:401 , TRP B:402 , ALA B:403 , HOH B:1033 , HOH B:1111BINDING SITE FOR RESIDUE GOL B 914
06AC6SOFTWAREARG A:210 , ALA A:211 , HOH A:1022 , PRO B:594 , PRO B:609 , HOH B:1212 , HOH B:1217BINDING SITE FOR RESIDUE GOL B 915
07AC7SOFTWAREGLN B:71 , LEU B:120 , GLU B:123 , ASN B:124 , ARG B:555BINDING SITE FOR RESIDUE GOL B 916
08AC8SOFTWAREARG B:44 , ARG B:45 , ARG B:48 , HOH B:1141 , HOH B:1160 , HOH B:1170 , HOH B:1179BINDING SITE FOR RESIDUE TLA B 917
09AC9SOFTWAREARG B:100 , TYR B:109 , ASN B:110 , PHE B:111 , ARG B:162 , NAG B:901BINDING SITE FOR RESIDUE SRT B 918
10BC1SOFTWAREARG B:48 , LYS B:86 , PRO B:467 , GLY B:468BINDING SITE FOR RESIDUE TLA B 919
11BC2SOFTWAREPRO B:302 , LEU B:303 , TRP B:312 , ARG B:313 , ARG B:363BINDING SITE FOR RESIDUE CL B 920
12BC3SOFTWAREASN A:110 , THR A:112 , HIS A:113BINDING SITE FOR MONO-SACCHARIDE NAG A 901 BOUND TO ASN A 110
13BC4SOFTWARETYR A:355 , HIS A:356 , GLN A:370 , ASN A:372 , VAL A:494 , PHE A:495 , HOH A:1047BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 372 RESIDUES 904 TO 908
14BC5SOFTWAREGLU A:274 , ASN A:415BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 415 RESIDUES 902 TO 903
15BC6SOFTWAREARG B:100 , ASN B:110 , THR B:112 , HIS B:113 , SRT B:918 , HOH B:1142 , HOH B:1218BINDING SITE FOR MONO-SACCHARIDE NAG B 901 BOUND TO ASN B 110
16BC7SOFTWAREPRO A:357 , LEU A:490 , GLY A:491 , ARG A:492 , PRO A:493 , VAL A:494 , PHE A:495 , LEU B:56 , TYR B:355 , HIS B:356 , GLN B:370 , ASN B:372 , VAL B:494 , PHE B:495 , GOL B:913 , HOH B:1018 , HOH B:1043 , HOH B:1100 , HOH B:1182 , HOH B:1235 , HOH B:1240BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 372 RESIDUES 905 TO 911
17BC8SOFTWAREGLU B:274 , ASN B:415BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 415 RESIDUES 902 TO 904

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (10, 10)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MJ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MJ2)

(-) Exons   (0, 0)

(no "Exon" information available for 4MJ2)

(-) 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......hhhhhhhhhhhhhhhhhh..eeee.hhhhh.......hhhhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhh.......hhhhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhh.............eeee......hhhhhhhhhhhhhhhhhhhhhhhh...eee............hhhhhhhhhhhhhhhhhhhhhhhh.........eeee...................eeeeee......eeeeeehhhhhhhhhhh....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
                 4mj2 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.....hhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhh.eee....eeehhhhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhh.......hhhhhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhh.............eeee......hhhhhhhhhhhhhhhhhhhhhhhh...eee............hhhhhhhhhhhhhhhhhhhhhhhh.........eeee...................eeeeee......eeeeeehhhhhhhhhhh....eeeeeeeee..ee......eeeeeeee.........eeeeeeee...........eeeeeeee........eeeeeeee....hhhhhhhhh......hhhhhhhhhh....ee...ee......eee..ee...eeeeeeee..........eeeeeeeee..eeeeeee........eeeeeeeee......ee.........eeee........eeeeeeeee...........eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mj2 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
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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 4MJ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MJ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MJ2)

(-) Gene Ontology  (15, 15)

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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 4mj4 4obr 4obs

(-) Related Entries Specified in the PDB File

4kgj
4kgl
4kh2
4mj4 P21 SPACE GROUP