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(-) Description

Title :  CRYSTAL STRUCTURE OF AN UNCHARACTERIZED METAL-DEPENDENT HYDROLASE FROM LACTOBACILLUS ACIDOPHILUS
 
Authors :  Y. Patskovsky, R. Toro, M. Dickey, S. Chang, J. M. Sauder, F. M. Raushel, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  03 Aug 09  (Deposition) - 18 Aug 09  (Release) - 18 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Amidohydrolase, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, M. Dickey, S. Chang, J. M. Sauder, F. M. Raushel, S. K. Burley, S. C. Almo
Crystal Structure Of An Uncharacterized Metal-Dependent Hydrolase From Lactobacillus Acidopphilus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED METAL-DEPENDENT HYDROLASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LBA1049
    Organism Scientific: LACTOBACILLUS ACIDOPHILUS
    Organism Taxid: 1579
    Synonym: PUTATIVE 4-OXALOMESACONATE HYDRATASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1NA4Ligand/IonSODIUM ION
2ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:10 , HIS A:160 , HIS A:204 , ASP A:262 , HOH A:357 , HOH A:358BINDING SITE FOR RESIDUE ZN A 312
2AC2SOFTWAREILE A:118 , ASP A:121 , LEU A:124 , GLU A:304BINDING SITE FOR RESIDUE NA A 313
3AC3SOFTWAREHIS B:10 , HIS B:160 , HIS B:204 , ASP B:262 , HOH B:394BINDING SITE FOR RESIDUE ZN B 312
4AC4SOFTWAREILE B:118 , ASP B:121 , LEU B:124 , HOH B:354BINDING SITE FOR RESIDUE NA B 313
5AC5SOFTWAREHIS C:10 , HIS C:160 , HIS C:204 , ASP C:262 , HOH C:329BINDING SITE FOR RESIDUE ZN C 312
6AC6SOFTWAREILE C:118 , ASP C:121 , GLU C:122 , LEU C:124BINDING SITE FOR RESIDUE NA C 313
7AC7SOFTWAREHIS D:10 , HIS D:160 , HIS D:204 , ASP D:262BINDING SITE FOR RESIDUE ZN D 312
8AC8SOFTWAREILE D:118 , ASP D:121 , LEU D:124 , HOH D:394BINDING SITE FOR RESIDUE NA D 313

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IJ6)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ala A:263 -Pro A:264
2Met A:268 -Pro A:269
3Ala B:263 -Pro B:264
4Met B:268 -Pro B:269
5Ala C:263 -Pro C:264
6Met C:268 -Pro C:269
7Ala D:263 -Pro D:264
8Met D:268 -Pro D:269

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IJ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IJ6)

(-) Exons   (0, 0)

(no "Exon" information available for 3IJ6)

(-) 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:303
 aligned with Q5FK79_LACAC | Q5FK79 from UniProtKB/TrEMBL  Length:304

    Alignment length:303
                                    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   
         Q5FK79_LACAC     2 TTKIDAYAHILPAKYYQKMLSVEPNIPNMFPFIKIKTLMDLDERLTKWPDQNTKQVISLANISPEDFTDSKTSAELCQSANEELSNLVDQHPGKFAGAVAILPMNNIESACKVISSIKDDENLVGAQIFTRHLGKSIADKEFRPVLAQAAKLHVPLWMHPVFDARKPDNNLVFSWEYELSQAMLQLVQSDLFQDYPNLKILVHHAGAMVPFFSGRIDHILDEKHAQDFKKFYVDTAILGNTPALQLAIDYYGIDHVLFGTDAPFAVMPSGADQIITQAINDLTISDKDKQKIFHDNYYSLIKE 304
               SCOP domains d3ij6a_ A: automated matches                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee...hhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhh..eeeeeee.ee..ee.....hhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhh....eee.hhhh....hhhhhhhhhhhhhhhhhhhheee.....hhhhhhhhhhhhh...ee.............hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ij6 A   2 LTKIDAYAHILPAKYYQKMLSVEPNIPNMFPFIKIKTLMDLDERLTKWPDQNTKQVISLANISPEDFTDSKTSAELCQSANEELSNLVDQHPGKFAGAVAILPMNNIESACKVISSIKDDENLVGAQIFTRHLGKSIADKEFRPVLAQAAKLHVPLWMHPVFDARKPDNNLVFSWEYELSQAMLQLVQSDLFQDYPNLKILVHHAGAMVPFFSGRIDHILDEKHAQDFKKFYVDTAILGNTPALQLAIDYYGIDHVLFGTDAPFAVMPSGADQIITQAINDLTISDKDKQKIFHDNYYSLIKE 304
                                    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   


Chain B from PDB  Type:PROTEIN  Length:303
 aligned with Q5FK79_LACAC | Q5FK79 from UniProtKB/TrEMBL  Length:304

    Alignment length:303
                                    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   
         Q5FK79_LACAC     2 TTKIDAYAHILPAKYYQKMLSVEPNIPNMFPFIKIKTLMDLDERLTKWPDQNTKQVISLANISPEDFTDSKTSAELCQSANEELSNLVDQHPGKFAGAVAILPMNNIESACKVISSIKDDENLVGAQIFTRHLGKSIADKEFRPVLAQAAKLHVPLWMHPVFDARKPDNNLVFSWEYELSQAMLQLVQSDLFQDYPNLKILVHHAGAMVPFFSGRIDHILDEKHAQDFKKFYVDTAILGNTPALQLAIDYYGIDHVLFGTDAPFAVMPSGADQIITQAINDLTISDKDKQKIFHDNYYSLIKE 304
               SCOP domains d3ij6b_ B: automated matches                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee...hhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh.....eeeeeee.ee..ee..hhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhh....eee.hhhh....hhhhhhhhhhhhhhhhhhhheee.....hhhhhhhhhhhhh...ee.............hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ij6 B   2 LTKIDAYAHILPAKYYQKMLSVEPNIPNMFPFIKIKTLMDLDERLTKWPDQNTKQVISLANISPEDFTDSKTSAELCQSANEELSNLVDQHPGKFAGAVAILPMNNIESACKVISSIKDDENLVGAQIFTRHLGKSIADKEFRPVLAQAAKLHVPLWMHPVFDARKPDNNLVFSWEYELSQAMLQLVQSDLFQDYPNLKILVHHAGAMVPFFSGRIDHILDEKHAQDFKKFYVDTAILGNTPALQLAIDYYGIDHVLFGTDAPFAVMPSGADQIITQAINDLTISDKDKQKIFHDNYYSLIKE 304
                                    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   


Chain C from PDB  Type:PROTEIN  Length:302
 aligned with Q5FK79_LACAC | Q5FK79 from UniProtKB/TrEMBL  Length:304

    Alignment length:302
                                    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  
         Q5FK79_LACAC     2 TTKIDAYAHILPAKYYQKMLSVEPNIPNMFPFIKIKTLMDLDERLTKWPDQNTKQVISLANISPEDFTDSKTSAELCQSANEELSNLVDQHPGKFAGAVAILPMNNIESACKVISSIKDDENLVGAQIFTRHLGKSIADKEFRPVLAQAAKLHVPLWMHPVFDARKPDNNLVFSWEYELSQAMLQLVQSDLFQDYPNLKILVHHAGAMVPFFSGRIDHILDEKHAQDFKKFYVDTAILGNTPALQLAIDYYGIDHVLFGTDAPFAVMPSGADQIITQAINDLTISDKDKQKIFHDNYYSLIK 303
               SCOP domains d3ij6c_ C: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhh......eeeeeee.ee..ee.....hhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhh....eee.........hhhhhhhhhhhhhhhhhhhheee.....hhhhhhhhhhhhh...ee.............hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ij6 C   2 LTKIDAYAHILPAKYYQKMLSVEPNIPNMFPFIKIKTLMDLDERLTKWPDQNTKQVISLANISPEDFTDSKTSAELCQSANEELSNLVDQHPGKFAGAVAILPMNNIESACKVISSIKDDENLVGAQIFTRHLGKSIADKEFRPVLAQAAKLHVPLWMHPVFDARKPDNNLVFSWEYELSQAMLQLVQSDLFQDYPNLKILVHHAGAMVPFFSGRIDHILDEKHAQDFKKFYVDTAILGNTPALQLAIDYYGIDHVLFGTDAPFAVMPSGADQIITQAINDLTISDKDKQKIFHDNYYSLIK 303
                                    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  


Chain D from PDB  Type:PROTEIN  Length:302
 aligned with Q5FK79_LACAC | Q5FK79 from UniProtKB/TrEMBL  Length:304

    Alignment length:302
                                    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  
         Q5FK79_LACAC     2 TTKIDAYAHILPAKYYQKMLSVEPNIPNMFPFIKIKTLMDLDERLTKWPDQNTKQVISLANISPEDFTDSKTSAELCQSANEELSNLVDQHPGKFAGAVAILPMNNIESACKVISSIKDDENLVGAQIFTRHLGKSIADKEFRPVLAQAAKLHVPLWMHPVFDARKPDNNLVFSWEYELSQAMLQLVQSDLFQDYPNLKILVHHAGAMVPFFSGRIDHILDEKHAQDFKKFYVDTAILGNTPALQLAIDYYGIDHVLFGTDAPFAVMPSGADQIITQAINDLTISDKDKQKIFHDNYYSLIK 303
               SCOP domains d3ij6d_ D: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee...hhhhh.hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhh..eeeeeee.ee..ee.....hhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhh....eee.........hhhhhhhhhhhhhhhhhhhheee.....hhhhhhhhhhhhh...ee.............hhhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ij6 D   2 LTKIDAYAHILPAKYYQKMLSVEPNIPNMFPFIKIKTLMDLDERLTKWPDQNTKQVISLANISPEDFTDSKTSAELCQSANEELSNLVDQHPGKFAGAVAILPMNNIESACKVISSIKDDENLVGAQIFTRHLGKSIADKEFRPVLAQAAKLHVPLWMHPVFDARKPDNNLVFSWEYELSQAMLQLVQSDLFQDYPNLKILVHHAGAMVPFFSGRIDHILDEKHAQDFKKFYVDTAILGNTPALQLAIDYYGIDHVLFGTDAPFAVMPSGADQIITQAINDLTISDKDKQKIFHDNYYSLIK 303
                                    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
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IJ6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IJ6)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5FK79_LACAC | Q5FK79)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  3ij6
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 Related Entries

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