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(-) Description

Title :  CRYSTAL STRUCTURE OF OLIGOGALACTURONATE LYASE (VPA0088) FROM VIBRIO PARAHAEMOLYTICUS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET VPR199
 
Authors :  F. Forouhar, M. Abashidze, J. Seetharaman, H. Janjua, L. Mao, R. Xiao, L. A. Owens, D. Wang, M. C. Baran, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  31 Jan 08  (Deposition) - 26 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  7 Blade-Shaped Beta-Propeller, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, M. Abashidze, J. Seetharaman, H. Janjua, L. Mao, R. Xiao, L. A. Owens, D. Wang, M. C. Baran, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of Oligogalacturonate Lyase (Vpa0088) From Vibrio Parahaemolyticus.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OLIGOGALACTURONATE LYASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VPA0088
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS RIMD 2210633
    Organism Taxid: 223926

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric Unit (2, 24)
No.NameCountTypeFull Name
1MN3Ligand/IonMANGANESE (II) ION
2MSE21Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 7)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:287 , GLN A:350 , HIS A:353 , HIS A:355BINDING SITE FOR RESIDUE MN A 401
2AC2SOFTWAREHIS B:287 , GLN B:350 , HIS B:353 , HIS B:355BINDING SITE FOR RESIDUE MN B 401
3AC3SOFTWAREHIS C:287 , GLN C:350 , HIS C:353 , HIS C:355BINDING SITE FOR RESIDUE MN C 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C5M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C5M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C5M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C5M)

(-) Exons   (0, 0)

(no "Exon" information available for 3C5M)

(-) 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:376
 aligned with Q87K10_VIBPA | Q87K10 from UniProtKB/TrEMBL  Length:388

    Alignment length:386
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381      
         Q87K10_VIBPA     2 AKGDVITLNFETFVDSDTQVKVTRLTPTDVICHRNYFYQKCFTQDGKKLLFAGDFDGNRNYYLLNLETQQAVQLTEGKGDNTFGGFISTDERAFFYVKNELNLMKVDLETLEEQVIYTVDEEWKGYGTWVANSDCTKLVGIEILKRDWQPLTSWEKFAEFYHTNPTCRLIKVDIETGELEVIHQDTAWLGHPIYRPFDDSTVGFCHEGPHDLVDARMWLVNEDGSNVRKIKEHAEGESCTHEFWIPDGSAMAYVSYFKGQTDRVIYKANPETLENEEVMVMPPCSHLMSNFDGSLMVGDGCDAPVDVADADSYNIENDPFLYVLNTKAKSAQKLCKHSTSWDVLDGDRQITHPHPSFTPNDDGVLFTSDFEGVPAIYIADVPESYK 387
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c5mA00 A:2-387 YVTN repeat-like/Quinoprotein amine dehydrogenase                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee......eeee.......ee..............eeeeee......eeeeee....eeee............ee.....eeeeee...eeeeee.....eeeeee....eeeeeeeee.....eeeeeeee.hhh....hhhhhhhhhhh...eeeeeee.....eeeeeee...eeeeeee..eeeeeeeee...........eeee......ee.......eeeeeeee......eeeeeee.....eeeeee......eeeeee...eeeeee.....eeeeee...----------......eeeeee.......eeee...................ee.....eeeeee......eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c5m A   2 AKGDVITLNFETFVDSDTQVKVTRLTPTDIICHRNYFYQKCFTQDGKKLLFAGDFDGNRNYYLLNLETQQAVQLTEGKGDNTFGGFISTDERAFFYVKNELNLmKVDLETLEEQVIYTVDEEWKGYGTWVANSDCTKLVGIEILKRDWQPLTSWEKFAEFYHTNPTCRLIKVDIETGELEVIHQDTAWLGHPIYRPFDDSTVGFCHEGPHDLVDARmWLVNEDGSNVRKIKEHAEGESCTHEFWIPDGSAmAYVSYFKGQTDRVIYKANPETLENEEVmVmPPCSHLmSNFDGSLmVGDGCDA----------NIENDPFLYVLNTKAKSAQKLCKHSTSWDVLDGDRQITHPHPSFTPNDDGVLFTSDFEGVPAIYIADVPESYK 387
                                    11        21        31        41        51        61        71        81        91       101   |   111       121       131       141       151       161       171       181       191       201       211      |221       231       241       251|      261       271       281|      291     | 301  |      -   |   321       331       341       351       361       371       381      
                                                                                                                                 105-MSE                                                                                                          218-MSE                           252-MSE                     280-MSE    |     297-MSE304        315                                                                        
                                                                                                                                                                                                                                                                                                                  282-MSE  |                                                                                                  
                                                                                                                                                                                                                                                                                                                         289-MSE                                                                                              


Chain B from PDB  Type:PROTEIN  Length:378
 aligned with Q87K10_VIBPA | Q87K10 from UniProtKB/TrEMBL  Length:388

    Alignment length:386
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381      
         Q87K10_VIBPA     2 AKGDVITLNFETFVDSDTQVKVTRLTPTDVICHRNYFYQKCFTQDGKKLLFAGDFDGNRNYYLLNLETQQAVQLTEGKGDNTFGGFISTDERAFFYVKNELNLMKVDLETLEEQVIYTVDEEWKGYGTWVANSDCTKLVGIEILKRDWQPLTSWEKFAEFYHTNPTCRLIKVDIETGELEVIHQDTAWLGHPIYRPFDDSTVGFCHEGPHDLVDARMWLVNEDGSNVRKIKEHAEGESCTHEFWIPDGSAMAYVSYFKGQTDRVIYKANPETLENEEVMVMPPCSHLMSNFDGSLMVGDGCDAPVDVADADSYNIENDPFLYVLNTKAKSAQKLCKHSTSWDVLDGDRQITHPHPSFTPNDDGVLFTSDFEGVPAIYIADVPESYK 387
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c5mB00 B:2-387 YVTN repeat-like/Quinoprotein amine dehydrogenase                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee......eeee.......ee..............eeeeee......eeeeee....eeee............ee.....eeeeee...eeeeee.....eeeeee....eeeeeeeee.....eeeeeeee.hhh....hhhhhhhhhhh...eeeeeee.....eeeeeee...eeeeeee..eeeeeeeee...........eeee......ee.......eeeeeeee......eeeeeee.....eeeeee......eeeeee...eeeeee.....eeeeee.....--------......eeeeee.......eeee...................ee.....eeeeee......eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c5m B   2 AKGDVITLNFETFVDSDTQVKVTRLTPTDIICHRNYFYQKCFTQDGKKLLFAGDFDGNRNYYLLNLETQQAVQLTEGKGDNTFGGFISTDERAFFYVKNELNLmKVDLETLEEQVIYTVDEEWKGYGTWVANSDCTKLVGIEILKRDWQPLTSWEKFAEFYHTNPTCRLIKVDIETGELEVIHQDTAWLGHPIYRPFDDSTVGFCHEGPHDLVDARmWLVNEDGSNVRKIKEHAEGESCTHEFWIPDGSAmAYVSYFKGQTDRVIYKANPETLENEEVmVmPPCSHLmSNFDGSLmVGDGCDAPV--------NIENDPFLYVLNTKAKSAQKLCKHSTSWDVLDGDRQITHPHPSFTPNDDGVLFTSDFEGVPAIYIADVPESYK 387
                                    11        21        31        41        51        61        71        81        91       101   |   111       121       131       141       151       161       171       181       191       201       211      |221       231       241       251|      261       271       281|      291     | 301    |    -   |   321       331       341       351       361       371       381      
                                                                                                                                 105-MSE                                                                                                          218-MSE                           252-MSE                     280-MSE    |     297-MSE  306      315                                                                        
                                                                                                                                                                                                                                                                                                                  282-MSE  |                                                                                                  
                                                                                                                                                                                                                                                                                                                         289-MSE                                                                                              


Chain C from PDB  Type:PROTEIN  Length:376
 aligned with Q87K10_VIBPA | Q87K10 from UniProtKB/TrEMBL  Length:388

    Alignment length:386
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381      
         Q87K10_VIBPA     2 AKGDVITLNFETFVDSDTQVKVTRLTPTDVICHRNYFYQKCFTQDGKKLLFAGDFDGNRNYYLLNLETQQAVQLTEGKGDNTFGGFISTDERAFFYVKNELNLMKVDLETLEEQVIYTVDEEWKGYGTWVANSDCTKLVGIEILKRDWQPLTSWEKFAEFYHTNPTCRLIKVDIETGELEVIHQDTAWLGHPIYRPFDDSTVGFCHEGPHDLVDARMWLVNEDGSNVRKIKEHAEGESCTHEFWIPDGSAMAYVSYFKGQTDRVIYKANPETLENEEVMVMPPCSHLMSNFDGSLMVGDGCDAPVDVADADSYNIENDPFLYVLNTKAKSAQKLCKHSTSWDVLDGDRQITHPHPSFTPNDDGVLFTSDFEGVPAIYIADVPESYK 387
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c5mC00 C:2-387 YVTN repeat-like/Quinoprotein amine dehydrogenase                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee...eeee......eeee.......ee..............eeeeee......eeeeee....eeee............ee.....eeeeee...eeeeee.....eeeeee....eeeeeeeee.....eeeeeeee.hhh....hhhhhhhhhhh...eeeeeee.....eeeeeee...eeeeeee..eeeeeeeee...........eeee......ee.......eeeeeeee......eeeeeee.....eeeeee......eeeeee...eeeeee.....eeeeee...----------......eeeeee.......eeee......hhhhh........ee.....eeeeee......eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c5m C   2 AKGDVITLNFETFVDSDTQVKVTRLTPTDIICHRNYFYQKCFTQDGKKLLFAGDFDGNRNYYLLNLETQQAVQLTEGKGDNTFGGFISTDERAFFYVKNELNLmKVDLETLEEQVIYTVDEEWKGYGTWVANSDCTKLVGIEILKRDWQPLTSWEKFAEFYHTNPTCRLIKVDIETGELEVIHQDTAWLGHPIYRPFDDSTVGFCHEGPHDLVDARmWLVNEDGSNVRKIKEHAEGESCTHEFWIPDGSAmAYVSYFKGQTDRVIYKANPETLENEEVmVmPPCSHLmSNFDGSLmVGDGCDA----------NIENDPFLYVLNTKAKSAQKLCKHSTSWDVLDGDRQITHPHPSFTPNDDGVLFTSDFEGVPAIYIADVPESYK 387
                                    11        21        31        41        51        61        71        81        91       101   |   111       121       131       141       151       161       171       181       191       201       211      |221       231       241       251|      261       271       281|      291     | 301  |      -   |   321       331       341       351       361       371       381      
                                                                                                                                 105-MSE                                                                                                          218-MSE                           252-MSE                     280-MSE    |     297-MSE304        315                                                                        
                                                                                                                                                                                                                                                                                                                  282-MSE  |                                                                                                  
                                                                                                                                                                                                                                                                                                                         289-MSE
   Legend:   → Mismatch (orange background)
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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 3C5M)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C5M)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q87K10_VIBPA | Q87K10)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0047487    oligogalacturonide lyase activity    Catalysis of the reaction: 4-(4-deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate = 2 5-dehydro-4-deoxy-D-glucuronate.
biological process
    GO:0045490    pectin catabolic process    The chemical reactions and pathways resulting in the breakdown of pectin, a polymer containing a backbone of alpha-1,4-linked D-galacturonic acid residues.

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