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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-GALACTOSIDASE FROM ASPERGILLUS ORYZAE IN COMPLEX WITH GALACTOSE
 
Authors :  M. Maksimainen, J. Rouvinen
Date :  21 Jan 13  (Deposition) - 31 Jul 13  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim Barrel, Glycoside Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Maksimainen, A. Lampio, M. Mertanen, O. Turunen, J. Rouvinen
The Crystal Structure Of Acidic Beta-Galactosidase From Aspergillus Oryzae.
Int. J. Biol. Macromol. V. 60C 109 2013
PubMed-ID: 23688418  |  Reference-DOI: 10.1016/J.IJBIOMAC.2013.05.003

(-) Compounds

Molecule 1 - BETA-GALACTOSIDASE A
    Chains: A
    EC Number: 3.2.1.23
    Engineered: YES
    Expression System: KLUYVEROMYCES LACTIS
    Expression System Taxid: 28985
    Gene: LACA
    Organism Common: YELLOW KOJI MOLD
    Organism Scientific: ASPERGILLUS ORYZAE
    Organism Taxid: 5062
    Synonym: LACTASE A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 67)

Asymmetric/Biological Unit (7, 67)
No.NameCountTypeFull Name
1BMA7Ligand/IonBETA-D-MANNOSE
2CD29Ligand/IonCADMIUM ION
3GAL1Ligand/IonBETA-D-GALACTOSE
4M6D1Ligand/Ion6-O-PHOSPHONO-BETA-D-MANNOPYRANOSE
5MAN13Ligand/IonALPHA-D-MANNOSE
6NAG15Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (66, 66)

Asymmetric Unit (66, 66)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:126 , CD A:1128 , NAG A:1164 , BMA A:1165BINDING SITE FOR RESIDUE CD A 1101
02AC2SOFTWAREGLU A:112 , GLU A:999 , BMA A:1160 , HOH A:3080BINDING SITE FOR RESIDUE CD A 1102
03AC3SOFTWAREASP A:803 , HOH A:3074 , HOH A:3075 , HOH A:3224BINDING SITE FOR RESIDUE CD A 1103
04AC4SOFTWAREGLU A:460 , GLU A:761 , HOH A:3076 , HOH A:3079BINDING SITE FOR RESIDUE CD A 1104
05AC5SOFTWAREASP A:547 , HOH A:3077 , HOH A:3078 , HOH A:3079 , HOH A:3250BINDING SITE FOR RESIDUE CD A 1105
06AC6SOFTWAREASP A:40BINDING SITE FOR RESIDUE CD A 1106
07AC7SOFTWAREASP A:122BINDING SITE FOR RESIDUE CD A 1107
08AC8SOFTWAREASN A:140 , GLU A:142 , GLU A:804 , GAL A:1130BINDING SITE FOR RESIDUE CD A 1108
09AC9SOFTWARETHR A:158 , ASP A:163BINDING SITE FOR RESIDUE CD A 1109
10BC1SOFTWAREASP A:214BINDING SITE FOR RESIDUE CD A 1110
11BC2SOFTWARETHR A:249 , NAG A:1148BINDING SITE FOR RESIDUE CD A 1111
12BC3SOFTWAREASP A:227BINDING SITE FOR RESIDUE CD A 1112
13BC4SOFTWAREGLU A:313 , HOH A:3159BINDING SITE FOR RESIDUE CD A 1113
14BC5SOFTWAREGLU A:322 , GLN A:438BINDING SITE FOR RESIDUE CD A 1114
15BC6SOFTWAREASP A:410 , GLU A:882BINDING SITE FOR RESIDUE CD A 1115
16BC7SOFTWAREASP A:410 , LYS A:446BINDING SITE FOR RESIDUE CD A 1116
17BC8SOFTWAREASP A:413 , GLU A:873 , CD A:1121BINDING SITE FOR RESIDUE CD A 1117
18BC9SOFTWAREASP A:530BINDING SITE FOR RESIDUE CD A 1118
19CC1SOFTWAREASP A:614BINDING SITE FOR RESIDUE CD A 1119
20CC2SOFTWAREGLU A:644BINDING SITE FOR RESIDUE CD A 1120
21CC3SOFTWAREASP A:413 , ASP A:676 , CD A:1117BINDING SITE FOR RESIDUE CD A 1121
22CC4SOFTWAREASP A:699BINDING SITE FOR RESIDUE CD A 1122
23CC5SOFTWAREASP A:711BINDING SITE FOR RESIDUE CD A 1123
24CC6SOFTWAREHIS A:707 , ASN A:815BINDING SITE FOR RESIDUE CD A 1124
25CC7SOFTWAREHIS A:355BINDING SITE FOR RESIDUE CD A 1125
26CC8SOFTWAREASP A:828 , SER A:830BINDING SITE FOR RESIDUE CD A 1126
27CC9SOFTWAREASP A:844BINDING SITE FOR RESIDUE CD A 1127
28DC1SOFTWAREASP A:899 , CD A:1101 , BMA A:1165BINDING SITE FOR RESIDUE CD A 1128
29DC2SOFTWAREGLU A:991 , M6D A:1163BINDING SITE FOR RESIDUE CD A 1129
30DC3SOFTWARETYR A:96 , ILE A:139 , ASN A:140 , ALA A:141 , GLU A:142 , ASN A:199 , GLU A:200 , ASN A:235 , ASP A:258 , TYR A:260 , GLU A:298 , PHE A:304 , TYR A:342 , TYR A:364 , CD A:1108BINDING SITE FOR RESIDUE GAL A 1130
31DC4SOFTWAREASP A:363 , THR A:369 , THR A:371 , ASN A:373 , TYR A:909 , THR A:980 , THR A:981 , NAG A:1132 , NAG A:1137 , HOH A:3066 , HOH A:3267BINDING SITE FOR RESIDUE NAG A 1131
32DC5SOFTWAREGLU A:313 , SER A:942 , NAG A:1131 , BMA A:1133 , HOH A:3266BINDING SITE FOR RESIDUE NAG A 1132
33DC6SOFTWARENAG A:1132 , MAN A:1134BINDING SITE FOR RESIDUE BMA A 1133
34DC7SOFTWAREASN A:911 , GLU A:976 , BMA A:1133 , MAN A:1135BINDING SITE FOR RESIDUE MAN A 1134
35DC8SOFTWAREMAN A:1134BINDING SITE FOR RESIDUE MAN A 1135
36DC9SOFTWAREASP A:279 , ASN A:402 , LEU A:403BINDING SITE FOR RESIDUE NAG A 1136
37EC1SOFTWARETYR A:603 , ASN A:622 , THR A:981 , NAG A:1131 , NAG A:1138 , HOH A:3014BINDING SITE FOR RESIDUE NAG A 1137
38EC2SOFTWARETHR A:375 , GLU A:377 , TYR A:571 , NAG A:1137 , BMA A:1139 , HOH A:3070BINDING SITE FOR RESIDUE NAG A 1138
39EC3SOFTWAREGLU A:377 , NAG A:1138 , MAN A:1140 , MAN A:1142 , HOH A:3042BINDING SITE FOR RESIDUE BMA A 1139
40EC4SOFTWAREGLU A:377 , ASN A:568 , BMA A:1139 , MAN A:1141 , HOH A:3242BINDING SITE FOR RESIDUE MAN A 1140
41EC5SOFTWAREHIS A:321 , GLU A:322 , ARG A:325 , MAN A:1140BINDING SITE FOR RESIDUE MAN A 1141
42EC6SOFTWAREASN A:320 , BMA A:1139 , MAN A:1143BINDING SITE FOR RESIDUE MAN A 1142
43EC7SOFTWAREMAN A:1142BINDING SITE FOR RESIDUE MAN A 1143
44EC8SOFTWARESER A:688 , ASN A:760 , ASN A:790 , TYR A:791 , VAL A:792 , NAG A:1145 , HOH A:3136BINDING SITE FOR RESIDUE NAG A 1144
45EC9SOFTWARETYR A:690 , ASN A:790 , NAG A:1144BINDING SITE FOR RESIDUE NAG A 1145
46FC1SOFTWAREARG A:746 , ASP A:775 , ASN A:777 , NAG A:1147BINDING SITE FOR RESIDUE NAG A 1146
47FC2SOFTWAREARG A:746 , NAG A:1146BINDING SITE FOR RESIDUE NAG A 1147
48FC3SOFTWAREASN A:914 , THR A:916 , PHE A:933 , GLY A:935 , VAL A:937 , GLY A:938 , PRO A:939 , GLN A:940 , THR A:941 , CD A:1111 , NAG A:1149BINDING SITE FOR RESIDUE NAG A 1148
49FC4SOFTWAREGLY A:248 , GLY A:308 , VAL A:937 , NAG A:1148 , BMA A:1150 , MAN A:1153 , HOH A:3257BINDING SITE FOR RESIDUE NAG A 1149
50FC5SOFTWAREGLY A:246 , GLY A:248 , ASP A:771 , TYR A:772 , NAG A:1149 , MAN A:1151 , MAN A:1152 , HOH A:3122BINDING SITE FOR RESIDUE BMA A 1150
51FC6SOFTWAREGLY A:246 , TYR A:772 , BMA A:1150 , MAN A:1156 , MAN A:1157BINDING SITE FOR RESIDUE MAN A 1151
52FC7SOFTWAREPRO A:245 , GLY A:246 , ALA A:251 , BMA A:1150 , MAN A:1153 , MAN A:1154 , HOH A:3094BINDING SITE FOR RESIDUE MAN A 1152
53FC8SOFTWAREGLY A:248 , THR A:249 , ALA A:267 , GLY A:308 , GLY A:309 , PRO A:310 , NAG A:1149 , MAN A:1152 , MAN A:1154BINDING SITE FOR RESIDUE MAN A 1153
54FC9SOFTWAREASP A:265 , GLY A:308 , MAN A:1152 , MAN A:1153 , MAN A:1155 , HOH A:3264BINDING SITE FOR RESIDUE MAN A 1154
55GC1SOFTWAREASP A:771 , MAN A:1154 , HOH A:3264BINDING SITE FOR RESIDUE MAN A 1155
56GC2SOFTWAREGLY A:241 , SER A:247 , GLN A:288 , MAN A:1151BINDING SITE FOR RESIDUE MAN A 1156
57GC3SOFTWAREMAN A:1151BINDING SITE FOR RESIDUE MAN A 1157
58GC4SOFTWAREGLU A:112 , LYS A:848 , GLU A:994 , PRO A:996 , BMA A:1159 , BMA A:1160BINDING SITE FOR RESIDUE NAG A 1158
59GC5SOFTWAREGLY A:113 , GLU A:994 , GLN A:995 , NAG A:1158 , NAG A:1161BINDING SITE FOR RESIDUE BMA A 1159
60GC6SOFTWAREARG A:110 , LYS A:848 , GLU A:999 , CD A:1102 , NAG A:1158 , BMA A:1162BINDING SITE FOR RESIDUE BMA A 1160
61GC7SOFTWAREPRO A:119 , PRO A:993 , GLU A:994 , GLN A:995 , BMA A:1159 , M6D A:1163BINDING SITE FOR RESIDUE NAG A 1161
62GC8SOFTWAREARG A:110 , BMA A:1160BINDING SITE FOR RESIDUE BMA A 1162
63GC9SOFTWAREASP A:122 , ARG A:953 , CD A:1129 , NAG A:1161 , NAG A:1164 , HOH A:3280BINDING SITE FOR RESIDUE M6D A 1163
64HC1SOFTWARECD A:1101 , M6D A:1163 , BMA A:1165 , HOH A:3214BINDING SITE FOR RESIDUE NAG A 1164
65HC2SOFTWARELEU A:79 , GLU A:126 , ASP A:899 , LYS A:902 , CD A:1101 , CD A:1128 , NAG A:1164 , NAG A:1166BINDING SITE FOR RESIDUE BMA A 1165
66HC3SOFTWAREHIS A:609 , ASP A:899 , PRO A:901 , LYS A:902 , ARG A:953 , BMA A:1165BINDING SITE FOR RESIDUE NAG A 1166

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:266 -A:315

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:136 -Ser A:137
2Tyr A:342 -Met A:343
3Ile A:456 -Pro A:457
4Gly A:938 -Pro A:939

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IUG)

(-) 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:957
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4iuga1 A:40-393 automated matches                                                                                                                                                                                                                                                                                                                       d4iuga2 A:394-566 automated matches                                                                                                                                          d4iuga3 A:567-663 automated matches                                                              d4iuga4 A:664-845 automated matches                                                                                                                                                   d4iuga5 A:846-1005 automated matches                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee....eee..eee.eeeeee.hhhh.hhhhhhhhhhhhhhh...eeeee.hhhhhh........hhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhh...............................eee....................hhhhhhhhhh.....eeeeee..........hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...hhhhh......................hhhhhhhhhhhhhhhhhhhhh.................eeeeeee.....eeeeeee.......eeee.eeeee..eeeee......eeee....eeeeeeeee..eeeeee..eeeeeeee..eeeeeeee....eeeeeee.....eeee......eeeee..eeeeeee.....eeeee..eeeeeeehhhhh.ee..............hhhhhhh..eee...eeeeeeee..eeeeeee....eeeeee.......eeee..eee..ee.....eeeee..........hhhhh..eeee.hhhhh........ee...................hhhhhh.....eeeeeeee......eeeeeee......eeeee..eeeeee.......eeeeeee........eeeeeeee.............hhhhh..eeeeeee...hhhhheeeee....................hhhhhhh...........ee..........eeeeeeeeeeee....ee..eeeee......eeeeeee..eeeeeee.......eeee.......eeeeeeeeeeee..........eeeee...ee..................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4iug A   40 DLLQDIVTWDDKSLFINGERIMLFSGEVHPFRLPVPSLWLDIFHKIRALGFNCVSFYIDWALLEGKPGDYRAEGIFALEPFFDAAKEAGIYLIARPGSYINAEVSGGGFPGWLQRVNGTLRSSDEPFLKATDNYIANAAAAVAKAQITNGGPVILYQPENEYSDADYMQYVMDQARKADIVVPFISNDASPSGHNAPGSGTGAVDIYGHDSYPLGFDCANPSVWPEGKLPDNFRTLHLEQSPSTPYSLLEFQAGAFDPWGGPGFEKCYALVNHEFSRVFYRNDLSFGVSTFNLYMTFGGTNWGNLGHPGGYTSYDYGSPITETRNVTREKYSDIKLLANFVKASPSYLTATPRNLTTGVYTDTSDLAVTPLIGDSPGSFFVVRHTDYSSQESTSYKLKLPTSAGNLTIPQLEGTLSLNGRDSKIHVVDYNVSGTNIIYSTAEVFTWKKFDGNKVLVLYGGPKEHHELAIASKSNVTIIEGSDSGIVSTRKGSSVIIGWDVSSTRRIVQVGDLRVFLLDRNsAYNYWVPELPTEGTSPGFSTSKTTASSIIVKAGYLLRGAHLDGADLHLTADFNATTPIEVIGAPTGAKNLFVNGEKASHTVDKNGIWSSEVKYAAPEIKLPGLKDLDWKYLDTLPEIKSSYDDSAWVSADLPKTKNTHRPLDTPTSLYSSDYGFHTGYLIYRGHFVANGKESEFFIRTQGGSAFGSSVWLNETYLGSWTGADYAMDGNSTYKLSQLESGKNYVITVVIDNLGLDENWTVGEETMKNPRGILSYKLSGQDASAITWKLTGNLGGEDYQDKVRGPLNEGGLYAERQGFHQPQPPSESWESGSPLEGLSKPGIGFYTAQFDLDLPKGWDVPLYFNFGNNTQAARAQLYVNGYQYGKFTGNVGPQTSFPVPEGILNYRGTNYVALSLWALESDGAKLGSFELSYTTPVLTGYGNVESPEQPKYEQRKGAY 1005
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199  ||   218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568|      578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998       
                                                                                                                                                                                            202|                                                                                                                                                                                                                                                                                                                                                                  569-SEP                                                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                                                                             212
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (4, 5)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Gly A:938 - Pro A:939   [ RasMol ]  
    Ile A:456 - Pro A:457   [ RasMol ]  
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