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(-) Description

Title :  STRUCTURE OF P. CITRINUM ALPHA 1,2-MANNOSIDASE REVEALS THE BASIS FOR DIFFERENCES IN SPECIFICITY OF THE ER AND GOLGI CLASS I ENZYMES
 
Authors :  Y. D. Lobsanov, F. Vallee, A. Imberty, T. Yoshida, P. Yip, A. Herscovics P. L. Howell
Date :  09 Jan 02  (Deposition) - 20 Feb 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  (Alpha/Alpha)7-Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. D. Lobsanov, F. Vallee, A. Imberty, T. Yoshida, P. Yip, A. Herscovics, P. L. Howell
Structure Of Penicillium Citrinum Alpha 1, 2-Mannosidase Reveals The Basis For Differences In Specificity Of The Endoplasmic Reticulum And Golgi Class I Enzymes.
J. Biol. Chem. V. 277 5620 2002
PubMed-ID: 11714724  |  Reference-DOI: 10.1074/JBC.M110243200

(-) 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  (4, 22)

Asymmetric Unit (4, 22)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2KIF2Ligand/IonKIFUNENSINE
3MAN6Ligand/IonALPHA-D-MANNOSE
4NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2KIF1Ligand/IonKIFUNENSINE
3MAN3Ligand/IonALPHA-D-MANNOSE
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2KIF1Ligand/IonKIFUNENSINE
3MAN3Ligand/IonALPHA-D-MANNOSE
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:115 , ASN A:182 , THR A:184 , SER A:185 , NAG A:601BINDING SITE FOR RESIDUE NAG A 600
02AC2SOFTWARENAG A:600BINDING SITE FOR RESIDUE NAG A 601
03AC3SOFTWAREASP A:359 , GLU A:362 , ASN A:366 , TRP A:429 , NAG A:701BINDING SITE FOR RESIDUE NAG A 700
04AC4SOFTWAREASP A:311 , ASP A:359 , TRP A:429 , NAG A:700 , MAN A:702 , HOH A:987BINDING SITE FOR RESIDUE NAG A 701
05AC5SOFTWAREPRO A:173 , ASN A:251 , NAG A:701 , MAN A:703 , MAN A:704BINDING SITE FOR RESIDUE MAN A 702
06AC6SOFTWAREASN A:251 , MAN A:702BINDING SITE FOR RESIDUE MAN A 703
07AC7SOFTWARELEU A:355 , TYR A:426 , MAN A:702BINDING SITE FOR RESIDUE MAN A 704
08AC8SOFTWARETRP A:431 , ASN A:438 , ARG A:442 , NAG A:801 , HOH A:1016BINDING SITE FOR RESIDUE NAG A 800
09AC9SOFTWARENAG A:800BINDING SITE FOR RESIDUE NAG A 801
10BC1SOFTWARESER B:115 , ASN B:182 , THR B:184 , SER B:185 , NAG B:601BINDING SITE FOR RESIDUE NAG B 600
11BC2SOFTWARENAG B:600BINDING SITE FOR RESIDUE NAG B 601
12BC3SOFTWAREASP B:359 , GLU B:362 , ASN B:366 , TRP B:429 , NAG B:701BINDING SITE FOR RESIDUE NAG B 700
13BC4SOFTWAREARG B:309 , ASP B:311 , ILE B:425 , TRP B:429 , NAG B:700 , MAN B:702BINDING SITE FOR RESIDUE NAG B 701
14BC5SOFTWAREPRO B:173 , NAG B:701 , MAN B:703 , MAN B:704BINDING SITE FOR RESIDUE MAN B 702
15BC6SOFTWAREMAN B:702BINDING SITE FOR RESIDUE MAN B 703
16BC7SOFTWARELEU B:355 , LYS B:423 , TYR B:426 , MAN B:702BINDING SITE FOR RESIDUE MAN B 704
17BC8SOFTWARETRP B:431 , ASN B:438 , ARG B:442 , NAG B:801BINDING SITE FOR RESIDUE NAG B 800
18BC9SOFTWARENAG B:800BINDING SITE FOR RESIDUE NAG B 801
19CC1SOFTWARETHR A:501 , KIF A:901 , HOH A:1026 , HOH A:1027 , HOH A:1028 , HOH A:1029BINDING SITE FOR RESIDUE CA A 550
20CC2SOFTWARETHR B:501 , KIF B:902 , HOH B:936 , HOH B:937 , HOH B:938 , HOH B:958BINDING SITE FOR RESIDUE CA B 551
21CC3SOFTWAREASP A:267 , LEU A:330 , ARG A:407 , GLU A:409 , PHE A:468 , GLU A:472 , THR A:501 , GLU A:502 , CA A:550 , HOH A:932 , HOH A:980 , HOH A:1026 , HOH A:1040 , HOH A:1041BINDING SITE FOR RESIDUE KIF A 901
22CC4SOFTWAREILE B:125 , ASP B:267 , LEU B:330 , ARG B:407 , GLU B:409 , PHE B:468 , GLU B:472 , THR B:501 , GLU B:502 , CA B:551 , HOH B:953 , HOH B:954 , HOH B:955BINDING SITE FOR RESIDUE KIF B 902

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:332 -A:361
2B:332 -B:361

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:60 -Pro A:61
2Gln A:233 -Pro A:234
3Phe B:60 -Pro B:61
4Gln B:233 -Pro B:234

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KRF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KRF)

(-) Exons   (0, 0)

(no "Exon" information available for 1KRF)

(-) 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 d1krfa_ A: Class I alpha-1;2-mannosidase, catalytic domain                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1krfA00 A:36-510  [code=1.50.10.50, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh....eee....eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh........eee....ee....eeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhh........eee.................hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhee.........ee.eee..eee.eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eee.hhhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhh.......hhhhhhhhhhhhhh................eee.....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1krf A  36 SNQAKADAVKEAFQHAWNGYMKYAFPHDELTPVSNGHADSRNGWGASAVDALSTAVIMGKADVVNAILEHVADIDFSKTSDTVSLFETTIRYLAGMLSGYDLLQGPAKNLVDNQDLIDGLLDQSRNLADVLKFAFDTPSGVPYNNINITSHGNDGATTNGLAVTGTLVLEWTRLSDLTGDEEYAKLSQKAESYLLKPQPSSSEPFPGLVGSSININDGQFADSRVSWNGGDDSFYEYLIKMYVYDPKRFETYKDRWVLAAESTIKHLKSHPKSRPDLTFLSSYSNRNYDLSSQHLTCFDGGSFLLGGTVLDRQDFIDFGLELVDGCEATYNSTLTKIGPDSWGWDPKKVPSDQKEFYEKAGFYISSGSYVLRPEVIESFYYAHRVTGKEIYRDWVWNAFVAINSTCRTDSGFAAVSDVNKANGGSKYDNQESFLFAEVMKYSYLAHSEDAAWQVQKGGKNTFVYNTEAHPISVAR 510
                                    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     


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 d1krfb_ B: Class I alpha-1;2-mannosidase, catalytic domain                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1krfB00 B:36-510  [code=1.50.10.50, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) -----------Glyco_hydro_47-1krfB01 B:47-508                                                                                                                                                                                                                                                                                                                                                                                                                                               -- Pfam domains (1)
           Pfam domains (2) -----------Glyco_hydro_47-1krfB02 B:47-508                                                                                                                                                                                                                                                                                                                                                                                                                                               -- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh....eee....eee......hhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh........eee....ee....eeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhh........eee.................hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhee.........ee.ee....ee.eee...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh........eee.hhhhh...hhhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhh.......hhhhhhhhhhhhhh................eee.....eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1krf B  36 SNQAKADAVKEAFQHAWNGYMKYAFPHDELTPVSNGHADSRNGWGASAVDALSTAVIMGKADVVNAILEHVADIDFSKTSDTVSLFETTIRYLAGMLSGYDLLQGPAKNLVDNQDLIDGLLDQSRNLADVLKFAFDTPSGVPYNNINITSHGNDGATTNGLAVTGTLVLEWTRLSDLTGDEEYAKLSQKAESYLLKPQPSSSEPFPGLVGSSININDGQFADSRVSWNGGDDSFYEYLIKMYVYDPKRFETYKDRWVLAAESTIKHLKSHPKSRPDLTFLSSYSNRNYDLSSQHLTCFDGGSFLLGGTVLDRQDFIDFGLELVDGCEATYNSTLTKIGPDSWGWDPKKVPSDQKEFYEKAGFYISSGSYVLRPEVIESFYYAHRVTGKEIYRDWVWNAFVAINSTCRTDSGFAAVSDVNKANGGSKYDNQESFLFAEVMKYSYLAHSEDAAWQVQKGGKNTFVYNTEAHPISVAR 510
                                    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
   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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  1krf
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 Related Entries

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

UniProtKB/Swiss-Prot
        MAN12_PENCI | P31723: 1kkt 1kre 2ri8 2ri9

(-) Related Entries Specified in the PDB File

1kkt STRUCTURE OF P. CITRINUM ALPHA 1,2-MANNOSIDASE REVEALS THE BASIS FOR DIFFERENCES IN SPECIFICITY OF THE ER AND GOLGI CLASS I ENZYMES
1kre STRUCTURE OF P. CITRINUM ALPHA 1,2-MANNOSIDASE REVEALS THE BASIS FOR DIFFERENCES IN SPECIFICITY OF THE ER AND GOLGI CLASS I ENZYMES