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(-) Description

Title :  MANNOSE-BINDING PROTEIN-A MUTANT (QPDWGH) COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE
 
Authors :  A. R. Kolatkar, W. I. Weis
Date :  30 Apr 98  (Deposition) - 17 Jun 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  1,2,3
Keywords :  Lectin, C-Type Lectin, Calcium-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Kolatkar, A. K. Leung, R. Isecke, R. Brossmer, K. Drickamer, W. I. Weis
Mechanism Of N-Acetylgalactosamine Binding To A C-Type Animal Lectin Carbohydrate-Recognition Domain.
J. Biol. Chem. V. 273 19502 1998
PubMed-ID: 9677372  |  Reference-DOI: 10.1074/JBC.273.31.19502
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANNOSE-BINDING PROTEIN-A
    Chains: 1, 2, 3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PINIIIOMPA2
    Expression System Taxid: 562
    Fragment: CLOSTRIPAIN FRAGMENT RESIDUES 73 - 226
    Mutation: YES
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: THE BACTERIALLY EXPRESSED MATERIAL WAS DIGESTED WITH CLOSTRIPAIN TO PRODUCE THE PROTEIN USED IN THE CRYSTAL STRUCTURE ANALYSIS
    Synonym: CL-QPDWGH

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : 123

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2CA9Ligand/IonCALCIUM ION
3CL3Ligand/IonCHLORIDE ION
4NA1Ligand/IonSODIUM ION
5NGA2Ligand/IonN-ACETYL-D-GALACTOSAMINE

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
0111UNKNOWNASP 1:161 , GLU 1:165 , ASP 1:188 , GLU 1:198 , ASP 1:199 , CA 1:227 , HOH 1:241CA BINDING SITE.
0211_01UNKNOWNASP 1:161 , GLU 1:165 , ASP 1:188 , GLU 1:198 , ASP 1:199 , CA 1:227 , HOH 1:241CA BINDING SITE.
0312UNKNOWNASP 2:161 , GLU 2:165 , ASP 2:188 , GLU 2:198 , ASP 2:199 , CA 2:227 , HOH 2:272CA BINDING SITE.
0412_02UNKNOWNASP 2:161 , GLU 2:165 , ASP 2:188 , GLU 2:198 , ASP 2:199 , CA 2:227 , HOH 2:272CA BINDING SITE.
0513UNKNOWNASP 3:161 , GLU 3:165 , ASP 3:188 , GLY 3:193 , LEU 3:194 , CA 3:227 , HOH 3:242CA BINDING SITE.
0613_03UNKNOWNASP 3:161 , GLU 3:165 , ASP 3:188 , GLY 3:193 , LEU 3:194 , CA 3:227 , HOH 3:242CA BINDING SITE.
0721UNKNOWNGLN 1:185 , ASP 1:187 , GLU 1:198 , ASN 1:210 , ASP 1:211 , CA 1:2 , A2G 1:1CA BINDING SITE.
0821_04UNKNOWNGLN 1:185 , ASP 1:187 , GLU 1:198 , ASN 1:210 , ASP 1:211 , CA 1:2 , A2G 1:1CA BINDING SITE.
0922UNKNOWNGLN 2:185 , ASP 2:187 , GLU 2:198 , ASN 2:210 , ASP 2:211 , CA 2:2 , NGA 2:1CA BINDING SITE.
1022_05UNKNOWNGLN 2:185 , ASP 2:187 , GLU 2:198 , ASN 2:210 , ASP 2:211 , CA 2:2 , NGA 2:1CA BINDING SITE.
1123UNKNOWNGLN 3:185 , ASP 3:187 , GLU 3:198 , ASN 3:210 , ASP 3:211 , CA 3:2 , NGA 3:1CA BINDING SITE.
1223_06UNKNOWNGLN 3:185 , ASP 3:187 , GLU 3:198 , ASN 3:210 , ASP 3:211 , CA 3:2 , NGA 3:1CA BINDING SITE.
1331UNKNOWNGLU 1:84 , CA 1:3 , HOH 1:228 , HOH 1:245 , HOH 1:274CA BINDING SITE.
1432UNKNOWNGLU 2:165 , ASP 2:199 , CA 2:3 , HOH 2:310 , HOH 2:311 , HOH 2:312CA BINDING SITE.
1533UNKNOWNGLU 3:84 , CA 3:3 , HOH 3:228 , HOH 1:239 , HOH 3:249CA BINDING SITE.
16AC1SOFTWARECA 1:2 , GLN 1:185 , ASP 1:187 , TRP 1:189 , GLU 1:198 , HIS 1:202 , ASN 1:210 , ASP 1:211 , HOH 1:327 , HOH 1:350BINDING SITE FOR RESIDUE A2G 1 1
17AC5SOFTWAREA2G 1:1 , GLN 1:185 , ASP 1:187 , GLU 1:198 , ASN 1:210 , ASP 1:211BINDING SITE FOR RESIDUE CA 1 2
18AC6SOFTWAREGLU 1:84 , GLU 1:165 , ASP 1:199 , HOH 1:228 , HOH 1:245 , HOH 1:274BINDING SITE FOR RESIDUE CA 1 3
19AC7SOFTWAREGLY 1:197 , ASP 1:199 , CYS 1:214BINDING SITE FOR RESIDUE CL 1 4
20AC8SOFTWAREASP 2:161 , GLU 2:165 , ASP 2:188 , GLU 2:198 , ASP 2:199 , HOH 2:272BINDING SITE FOR RESIDUE CA 2 227
21AC9SOFTWARENGA 2:1 , GLN 2:185 , ASP 2:187 , GLU 2:198 , ASN 2:210 , ASP 2:211BINDING SITE FOR RESIDUE CA 2 2
22BC1SOFTWAREGLU 2:165 , ASP 2:199 , HOH 2:293 , HOH 2:310 , HOH 2:311 , HOH 2:312BINDING SITE FOR RESIDUE CA 2 3
23BC2SOFTWAREGLY 2:197 , ASP 2:199 , CYS 2:214BINDING SITE FOR RESIDUE CL 2 4
24BC6SOFTWAREASP 3:199 , CYS 3:214BINDING SITE FOR RESIDUE CL 3 4
25BC7SOFTWAREHIS 1:99 , HOH 1:309 , HIS 2:99 , HIS 3:99BINDING SITE FOR RESIDUE NA 2 5

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
11:128 -1:222
21:200 -1:214
32:128 -2:222
42:200 -2:214
53:128 -3:222
63:200 -3:214

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gln 1:185 -Pro 1:186
2Gln 2:185 -Pro 2:186
3Gln 3:185 -Pro 3:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.MBL1_RAT123-235
 
 		  31:106-223
2:106-223
3:106-223
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.MBL1_RAT212-234
 
 		  31:200-222
2:200-222
3:200-222

(-) Exons   (3, 9)

Asymmetric/Biological Unit (3, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000157231ENSRNOE00000411163chr16:17591820-1759188162MBL1_RAT-00--
1.2ENSRNOT000000157232ENSRNOE00000110617chr16:17593783-17593943161MBL1_RAT1-51510--
1.3ENSRNOT000000157233ENSRNOE00000110943chr16:17594301-17594417117MBL1_RAT51-904031:73-73
2:73-73
3:73-73		1
1
1
1.4ENSRNOT000000157234ENSRNOE00000111237chr16:17596168-1759624275MBL1_RAT90-1152631:73-98
2:73-98
3:73-98		26
26
26
1.5ENSRNOT000000157235ENSRNOE00000111555chr16:17597083-17597859777MBL1_RAT115-23812431:98-226
2:98-226
3:98-226		129
129
129

(-) 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 1 from PDB  Type:PROTEIN  Length:154
 aligned with MBL1_RAT | P19999 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:154
                                                                                                                                                    207                               
                                                                                                                                             205 206  |                               
                                    99       109       119       129       139       149       159       169       179       189       199     | 206  |    214       224       234    
             MBL1_RAT    90 AIEVKLANMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDEPND---H--GSGEDCVTIVDNGLWNDISCQASHTAVCEFPA 238
               SCOP domains d1bch12 1:73-104                d1bch11 1:105-226 Mannose-binding protein A, C-lectin domain                                                               SCOP domains
               CATH domains 1bch100 1:73-226 Mannose-Binding Protein A, subunit A                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee......hhhhhhhhhh..........hhhhhhhhhhh................................................eeee.....eeee........eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------C_TYPE_LECTIN_2  PDB: 1:106-223 UniProt: 123-235                                                                      --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        ---- PROSITE (2)
           Transcript 1 (1) 1------------------------Exon 1.5  PDB: 1:98-226 UniProt: 115-238                                                                                          Transcript 1 (1)
           Transcript 1 (2) Exon 1.4  PDB: 1:73-98    -------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1bch 1  73 AIEVKLANMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDQPDDWYGHGLGGGEDCVHIVDNGLWNDISCQASHTAVCEFPA 226
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222    


Chain 2 from PDB  Type:PROTEIN  Length:154
 aligned with MBL1_RAT | P19999 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:154
                                                                                                                                                    207                               
                                                                                                                                             205 206  |                               
                                    99       109       119       129       139       149       159       169       179       189       199     | 206  |    214       224       234    
             MBL1_RAT    90 AIEVKLANMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDEPND---H--GSGEDCVTIVDNGLWNDISCQASHTAVCEFPA 238
               SCOP domains d1bch22 2:73-104                d1bch21 2:105-226 Mannose-binding protein A, C-lectin domain                                                               SCOP domains
               CATH domains 1bch200 2:73-226 Mannose-Binding Protein A, subunit A                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee...eeehhhhhhhhhh..........hhhhhhhhhhh................................................eeee.....eeee....eee.eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------C_TYPE_LECTIN_2  PDB: 2:106-223 UniProt: 123-235                                                                      --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        ---- PROSITE (2)
           Transcript 1 (1) 1------------------------Exon 1.5  PDB: 2:98-226 UniProt: 115-238                                                                                          Transcript 1 (1)
           Transcript 1 (2) Exon 1.4  PDB: 2:73-98    -------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1bch 2  73 AIEVKLANMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDQPDDWYGHGLGGGEDCVHIVDNGLWNDISCQASHTAVCEFPA 226
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222    


Chain 3 from PDB  Type:PROTEIN  Length:154
 aligned with MBL1_RAT | P19999 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:154
                                                                                                                                                    207                               
                                                                                                                                             205 206  |                               
                                    99       109       119       129       139       149       159       169       179       189       199     | 206  |    214       224       234    
             MBL1_RAT    90 AIEVKLANMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDEPND---H--GSGEDCVTIVDNGLWNDISCQASHTAVCEFPA 238
               SCOP domains d1bch32 3:73-104                d1bch31 3:105-226 Mannose-binding protein A, C-lectin domain                                                               SCOP domains
               CATH domains 1bch300 3:73-226 Mannose-Binding Protein A, subunit A                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee...eeehhhhhhhhhhh.........hhhhhhhhhhh...eeeeee.......................................eeee.....eeee....eee.eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------C_TYPE_LECTIN_2  PDB: 3:106-223 UniProt: 123-235                                                                      --- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1        ---- PROSITE (2)
           Transcript 1 (1) 1------------------------Exon 1.5  PDB: 3:98-226 UniProt: 115-238                                                                                          Transcript 1 (1)
           Transcript 1 (2) Exon 1.4  PDB: 3:73-98    -------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1bch 3  73 AIEVKLANMEAEINTLKSKLELTNKLHAFSMGKKSGKKFFVTNHERMPFSKVKALCSELRGTVAIPRNAEENKAIQEVAKTSAFLGITDEVTEGQFMYVTGGRLTYSNWKKDQPDDWYGHGLGGGEDCVHIVDNGLWNDISCQASHTAVCEFPA 226
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
   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  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BCH)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain 1,2,3   (MBL1_RAT | P19999)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0048306    calcium-dependent protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in the presence of calcium.
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
    GO:0070273    phosphatidylinositol-4-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' position.
    GO:0030247    polysaccharide binding    Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    GO:0001867    complement activation, lectin pathway    Any process involved in the activation of any of the steps of the lectin pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0051873    killing by host of symbiont cells    Any process mediated by an organism that results in the death of cells in the symbiont organism. The symbiont is defined as the smaller of the organisms involved in a symbiotic interaction.
    GO:0044130    negative regulation of growth of symbiont in host    Any process in which the symbiont stops, prevents or reduces its increase in size or mass within the cells or tissues of the host organism. The host is defined as the larger of the organisms involved in the symbiotic interaction.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0070207    protein homotrimerization    The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits.
cellular component
    GO:0005581    collagen trimer    A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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

UniProtKB/Swiss-Prot
        MBL1_RAT | P19999: 1afa 1afb 1afd 1bcj 1buu 1fif 1fih 1kmb 1kwt 1kwu 1kwv 1kww 1kwx 1kwy 1kwz 1kx0 1kx1 1msb 1rtm 1ytt 2kmb 2msb 3kmb 4kmb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BCH)