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(-) Description

Title :  PENICILLIUM CITRINUM ALPHA-1,2-MANNOSIDASE IN COMPLEX WITH A SUBSTRATE ANALOG
 
Authors :  Y. D. Lobsanov, T. Yoshida, T. Desmet, W. Nerinckx, P. Yip, M. Claeyssen A. Herscovics, P. L. Howell
Date :  10 Oct 07  (Deposition) - 25 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alternative Conformations, Modulation Of Activity, Glycoprotein, Glycosidase, Hydrolase, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. D. Lobsanov, T. Yoshida, T. Desmet, W. Nerinckx, P. Yip, M. Claeyssens, A. Herscovics, P. L. Howell
Modulation Of Activity By Arg407: Structure Of A Fungal Alpha-1, 2-Mannosidase In Complex With A Substrate Analogue.
Acta Crystallogr. , Sect. D V. 64 227 2008
PubMed-ID: 18323617  |  Reference-DOI: 10.1107/S0907444907065572

(-) Compounds

Molecule 1 - MANNOSYL-OLIGOSACCHARIDE ALPHA-1,2-MANNOSIDASE
    Chains: A, B
    EC Number: 3.2.1.113
    Engineered: YES
    Expression System: ASPERGILLUS ORYZAE
    Expression System Plasmid: PTAPM1
    Expression System Strain: MS2
    Expression System Taxid: 5062
    Expression System Vector Type: PLASMID
    Gene: MSDC
    Organism Scientific: PENICILLIUM CITRINUM
    Organism Taxid: 5077
    Synonym: MAN(9)-ALPHA-MANNOSIDASE

 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, 28)

Asymmetric Unit (7, 28)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL4Ligand/IonGLYCEROL
3LDY2Ligand/IonALPHA-D-LYXOPYRANOSE
4MAN6Ligand/IonALPHA-D-MANNOSE
5MMA2Ligand/IonO1-METHYL-MANNOSE
6NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
7NDG3Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 1 (6, 13)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3LDY1Ligand/IonALPHA-D-LYXOPYRANOSE
4MAN3Ligand/IonALPHA-D-MANNOSE
5MMA1Ligand/IonO1-METHYL-MANNOSE
6NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
7NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
Biological Unit 2 (6, 13)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL2Ligand/IonGLYCEROL
3LDY1Ligand/IonALPHA-D-LYXOPYRANOSE
4MAN3Ligand/IonALPHA-D-MANNOSE
5MMA1Ligand/IonO1-METHYL-MANNOSE
6NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
7NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:207 , HOH A:463 , HOH A:530 , HOH A:637 , HOH A:671 , SER A:1115 , ASP A:1116 , THR A:1117 , ASN A:1182 , THR A:1184 , SER A:1185BINDING SITE FOR RESIDUE NAG A 1600
02AC2SOFTWAREHOH A:530 , HOH A:616BINDING SITE FOR RESIDUE NAG A 1601
03AC3SOFTWAREHOH A:453 , HOH A:589 , ASP A:1359 , GLU A:1362 , ASN A:1366 , TRP A:1429BINDING SITE FOR RESIDUE NAG A 1700
04AC4SOFTWAREHOH A:97 , HOH A:453 , ASP A:1311 , TRP A:1429BINDING SITE FOR RESIDUE NDG A 1701
05AC5SOFTWAREHOH A:192 , HOH A:199 , PRO A:1173BINDING SITE FOR RESIDUE MAN A 1702
06AC6SOFTWAREHOH A:527 , HOH A:549BINDING SITE FOR RESIDUE MAN A 1703
07AC7SOFTWAREHOH A:275 , HOH A:408 , HOH A:479 , LEU A:1355 , TYR A:1426BINDING SITE FOR RESIDUE MAN A 1704
08AC8SOFTWAREHOH A:411 , TRP A:1431 , ASN A:1438 , ARG A:1442BINDING SITE FOR RESIDUE NAG A 1800
09AC9SOFTWAREHOH A:400 , ARG A:1442BINDING SITE FOR RESIDUE NAG A 1801
10BC1SOFTWAREHOH A:33 , HOH A:154 , HOH A:155 , HOH A:231 , HOH A:361 , ARG A:1126 , ARG A:1407 , PHE A:1468 , GLU A:1472 , THR A:1501 , GLU A:1502BINDING SITE FOR RESIDUE LDY A 1900
11BC2SOFTWAREHOH A:33 , HOH A:361 , HOH A:398 , HOH A:625 , HOH A:718 , PHE A:1121 , ALA A:1197 , GLY A:1265 , ASP A:1267BINDING SITE FOR RESIDUE MMA A 1901
12BC3SOFTWAREHOH B:225 , SER B:2115 , ASN B:2182 , THR B:2184 , SER B:2185BINDING SITE FOR RESIDUE NAG B 2600
13BC4SOFTWAREHOH B:373 , ASP B:2359 , GLU B:2362 , ASN B:2366 , TRP B:2429BINDING SITE FOR RESIDUE NAG B 2700
14BC5SOFTWAREHOH B:373 , ARG B:2309 , ASP B:2311 , LEU B:2312 , ILE B:2425 , TRP B:2429BINDING SITE FOR RESIDUE NDG B 2701
15BC6SOFTWAREHOH B:375 , HOH B:540 , HOH B:623BINDING SITE FOR RESIDUE MAN B 2702
16BC7SOFTWAREHOH B:249 , HOH B:320BINDING SITE FOR RESIDUE MAN B 2703
17BC8SOFTWAREHOH B:375 , HOH B:417 , ASP B:2352 , LYS B:2423BINDING SITE FOR RESIDUE MAN B 2704
18BC9SOFTWAREHOH B:358 , HOH B:596 , ASN B:2438 , ARG B:2442BINDING SITE FOR RESIDUE NAG B 2800
19CC1SOFTWAREHOH B:596BINDING SITE FOR RESIDUE NDG B 2801
20CC2SOFTWAREHOH B:185 , HOH B:383 , HOH B:456 , ILE B:2125 , ARG B:2126 , ARG B:2407 , PHE B:2468 , GLU B:2472 , THR B:2501 , GLU B:2502BINDING SITE FOR RESIDUE LDY B 2900
21CC3SOFTWAREHOH B:185 , HOH B:719 , PHE B:2121 , ALA B:2197 , GLY B:2265 , ASP B:2267BINDING SITE FOR RESIDUE MMA B 2901
22CC4SOFTWAREHOH A:154 , HOH A:155 , HOH A:156 , HOH A:157 , THR A:1501BINDING SITE FOR RESIDUE CA A 1550
23CC5SOFTWAREHOH B:159 , HOH B:160 , HOH B:161 , HOH B:187 , THR B:2501BINDING SITE FOR RESIDUE CA B 2551
24CC6SOFTWAREHOH A:33 , ALA A:1197 , GLY A:1265 , ASP A:1267BINDING SITE FOR RESIDUE GOL A 1902
25CC7SOFTWAREHOH A:33 , HOH A:155 , HOH A:361 , ARG A:1126 , PHE A:1468 , GLU A:1472 , THR A:1501 , GLU A:1502BINDING SITE FOR RESIDUE GOL A 1903
26CC8SOFTWAREHOH B:185 , PHE B:2121 , ALA B:2197 , GLY B:2265 , ASP B:2267BINDING SITE FOR RESIDUE GOL B 2902
27CC9SOFTWAREHOH B:185 , HOH B:456 , ARG B:2126 , PHE B:2468 , GLU B:2472 , THR B:2501 , GLU B:2502BINDING SITE FOR RESIDUE GOL B 2903

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:1332 -A:1361
2B:2332 -B:2361

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:1060 -Pro A:1061
2Gln A:1233 -Pro A:1234
3Phe B:2060 -Pro B:2061
4Gln B:2233 -Pro B:2234

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RI9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RI9)

(-) Exons   (0, 0)

(no "Exon" information available for 2RI9)

(-) 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:475
 aligned with MAN12_PENCI | P31723 from UniProtKB/Swiss-Prot  Length:511

    Alignment length:475
                                    45        55        65        75        85        95       105       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     
         MAN12_PENCI     36 SNQAKADAVKEAFQHAWNGYMKYAFPHDELTPVSNGHADSRNGWGASAVDALSTAVIMGKADVVNAILEHVADIDFSKTSDTVSLFETTIRYLAGMLSGYDLLQGPAKNLVDNQDLIDGLLDQSRNLADVLKFAFDTPSGVPYNNINITSHGNDGATTNGLAVTGTLVLEWTRLSDLTGDEEYAKLSQKAESYLLKPQPSSSEPFPGLVGSSININDGQFADSRVSWNGGDDSFYEYLIKMYVYDPKRFETYKDRWVLAAESTIKHLKSHPKSRPDLTFLSSYSNRNYDLSSQHLTCFDGGSFLLGGTVLDRQDFIDFGLELVDGCEATYNSTLTKIGPDSWGWDPKKVPSDQKEFYEKAGFYISSGSYVLRPEVIESFYYAHRVTGKEIYRDWVWNAFVAINSTCRTDSGFAAVSDVNKANGGSKYDNQESFLFAEVMKYSYLAHSEDAAWQVQKGGKNTFVYNTEAHPISVAR  510
               SCOP domains d2ri9a_ A: Class I alpha-1;2-mannosidase, catalytic domain                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2ri9A00 A:1036-1510  [code=1.50.10.50, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh....eee....eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh........ee...........eeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhh........eee................hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhee.........ee.eee..eee.eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee......hhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh.......hhhhhhhhhhhhhh................eee.....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ri9 A 1036 SNQAKADAVKEAFQHAWNGYMKYAFPHDELTPVSNGHADSRNGWGASAVDALSTAVIMGKADVVNAILEHVADIDFSKTSDTVSLFETTIRYLAGMLSGYDLLQGPAKNLVDNQDLIDGLLDQSRNLADVLKFAFDTPSGVPYNNINITSHGNDGATTNGLAVTGTLVLEWTRLSDLTGDEEYAKLSQKAESYLLKPQPSSSEPFPGLVGSSININDGQFADSRVSWNGGDDSFYEYLIKMYVYDPKRFETYKDRWVLAAESTIKHLKSHPKSRPDLTFLSSYSNRNYDLSSQHLTCFDGGSFLLGGTVLDRQDFIDFGLELVDGCEATYNSTLTKIGPDSWGWDPKKVPSDQKEFYEKAGFYISSGSYVLRPEVIESFYYAHRVTGKEIYRDWVWNAFVAINSTCRTDSGFAAVSDVNKANGGSKYDNQESFLFAEVMKYSYLAHSEDAAWQVQKGGKNTFVYNTEAHPISVAR 1510
                                  1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175      1185      1195      1205      1215      1225      1235      1245      1255      1265      1275      1285      1295      1305      1315      1325      1335      1345      1355      1365      1375      1385      1395      1405      1415      1425      1435      1445      1455      1465      1475      1485      1495      1505     


Chain B from PDB  Type:PROTEIN  Length:475
 aligned with MAN12_PENCI | P31723 from UniProtKB/Swiss-Prot  Length:511

    Alignment length:475
                                    45        55        65        75        85        95       105       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     
         MAN12_PENCI     36 SNQAKADAVKEAFQHAWNGYMKYAFPHDELTPVSNGHADSRNGWGASAVDALSTAVIMGKADVVNAILEHVADIDFSKTSDTVSLFETTIRYLAGMLSGYDLLQGPAKNLVDNQDLIDGLLDQSRNLADVLKFAFDTPSGVPYNNINITSHGNDGATTNGLAVTGTLVLEWTRLSDLTGDEEYAKLSQKAESYLLKPQPSSSEPFPGLVGSSININDGQFADSRVSWNGGDDSFYEYLIKMYVYDPKRFETYKDRWVLAAESTIKHLKSHPKSRPDLTFLSSYSNRNYDLSSQHLTCFDGGSFLLGGTVLDRQDFIDFGLELVDGCEATYNSTLTKIGPDSWGWDPKKVPSDQKEFYEKAGFYISSGSYVLRPEVIESFYYAHRVTGKEIYRDWVWNAFVAINSTCRTDSGFAAVSDVNKANGGSKYDNQESFLFAEVMKYSYLAHSEDAAWQVQKGGKNTFVYNTEAHPISVAR  510
               SCOP domains d2ri9b_ B: Class I alpha-1;2-mannosidase, catalytic domain                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2ri9B00 B:2036-2510  [code=1.50.10.50, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) -----------Glyco_hydro_47-2ri9B01 B:2047-2508                                                                                                                                                                                                                                                                                                                                                                                                                                            -- Pfam domains (1)
           Pfam domains (2) -----------Glyco_hydro_47-2ri9B02 B:2047-2508                                                                                                                                                                                                                                                                                                                                                                                                                                            -- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh....eee....eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh........ee...........eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhh........eee................hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..............ee....ee.eee.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........eee......hhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh.......hhhhhhhhhhhhhh................eee.....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2ri9 B 2036 SNQAKADAVKEAFQHAWNGYMKYAFPHDELTPVSNGHADSRNGWGASAVDALSTAVIMGKADVVNAILEHVADIDFSKTSDTVSLFETTIRYLAGMLSGYDLLQGPAKNLVDNQDLIDGLLDQSRNLADVLKFAFDTPSGVPYNNINITSHGNDGATTNGLAVTGTLVLEWTRLSDLTGDEEYAKLSQKAESYLLKPQPSSSEPFPGLVGSSININDGQFADSRVSWNGGDDSFYEYLIKMYVYDPKRFETYKDRWVLAAESTIKHLKSHPKSRPDLTFLSSYSNRNYDLSSQHLTCFDGGSFLLGGTVLDRQDFIDFGLELVDGCEATYNSTLTKIGPDSWGWDPKKVPSDQKEFYEKAGFYISSGSYVLRPEVIESFYYAHRVTGKEIYRDWVWNAFVAINSTCRTDSGFAAVSDVNKANGGSKYDNQESFLFAEVMKYSYLAHSEDAAWQVQKGGKNTFVYNTEAHPISVAR 2510
                                  2045      2055      2065      2075      2085      2095      2105      2115      2125      2135      2145      2155      2165      2175      2185      2195      2205      2215      2225      2235      2245      2255      2265      2275      2285      2295      2305      2315      2325      2335      2345      2355      2365      2375      2385      2395      2405      2415      2425      2435      2445      2455      2465      2475      2485      2495      2505
   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  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: 6_Hairpin (120)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MAN12_PENCI | P31723)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004571    mannosyl-oligosaccharide 1,2-alpha-mannosidase activity    Catalysis of the hydrolysis of the terminal (1->2)-linked alpha-D-mannose residues in an oligo-mannose oligosaccharide.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006486    protein glycosylation    A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  2ri9
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  MAN12_PENCI | P31723
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  3.2.1.113
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  MAN12_PENCI | P31723
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        MAN12_PENCI | P31723: 1kkt 1kre 1krf 2ri8

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1kkt 1kre 1krf 2ri8