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(-) Description

Title :  X-RAY STRUCTURE OF NATIVE PEPTIDE AMIDASE FROM STENOTROPHOMONAS MALTOPHILIA AT 1.4 A
 
Authors :  J. Labahn, S. Neumann, G. Buldt, M. -R. Kula, J. Granzin
Date :  21 Jun 02  (Deposition) - 16 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Eleven-Stranded Beta Sheet, Covered Double Layers Of Alpha Helices On Top And Bottom, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Labahn, S. Neumann, G. Buldt, M. -R. Kula, J. Granzin
An Alternative Mechanism For Amidase Signature Enzymes
J. Mol. Biol. V. 322 1053 2002
PubMed-ID: 12367528  |  Reference-DOI: 10.1016/S0022-2836(02)00886-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE AMIDASE
    Chains: A, B
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEK06
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: STENOTROPHOMONAS MALTOPHILIA
    Organism Taxid: 40324
    Synonym: PAM

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:248 , PHE A:256 , ASP A:285 , PRO A:286 , ALA A:287 , LEU A:417 , HOH A:2192 , HOH A:2199 , HOH A:2335 , HOH A:2432 , HOH A:2601BINDING SITE FOR RESIDUE EPE A 2001
2AC2SOFTWAREARG B:248 , PHE B:256 , ASP B:285 , PRO B:286 , ALA B:287 , HOH B:3204 , HOH B:3211 , HOH B:3243 , HOH B:3441BINDING SITE FOR RESIDUE EPE B 3001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M22)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:129 -Pro A:130
2Gly A:201 -Ser A:202
3Ala B:129 -Pro B:130
4Gly B:201 -Ser B:202

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M22)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M22)

(-) Exons   (0, 0)

(no "Exon" information available for 1M22)

(-) 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:487
 aligned with Q8RJN5_STEMA | Q8RJN5 from UniProtKB/TrEMBL  Length:540

    Alignment length:490
                                    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       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531
         Q8RJN5_STEMA    42 PFPYAETDVADLQARMTAGELDSTTLTQAYLQRIAALDRTGPRLRAVIELNPDALKEAAERDRERRDGRLRGPLHGIPLLLKDNINAAPMATSAGSLALQGFRPDDAYLVRRLRDAGAVVLGKTNLSEWANFRGNDSISGWSARGGQTRNPYRISHSPCGSSSGSAVAVAANLASVAIGTETDGSIVCPAAINGVVGLKPTVGLVSRDGIIPISFSQDTAGPMARSVADAAAVLTAIAGRDDADPATATMPGRAVYDYTARLDPQGLRGKRIGLLQTPLLKYRGMPPLIEQAATELRRAGAVVVPVELPNQGAWAEAERTLLLYEFKAGLERYFNTHRAPLRSLADLIAFNQAHSKQELGLFGQELLVEADATAGLADPAYIRARSDARRLAGPEGIDAALAAHQLDALVAPTTGVAWPIRSEGDDFPGESYSAAAVAGYPSLTVPMGQIDGLPVGLLFMGTAWSEPKLIEMAYAYEQRTRARRPPHFDT 531
               SCOP domains d1m22a_ A: Peptide amidase Pam                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1m22A00 A:42-531 Amidase signature (AS) enzymes                                                                                                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh...hhhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhh..........eeeee.............hhhhh......hhhhhhhhhh..eeeeee..hhhhhh........ee...ee..............hhhhhhhhhh....eeeeee....hhhhhhhh..eeee...................eeeeee.hhhhhhhhhhhhh.....hhhhhhh......hhhhhh........eeeee.hhhhhh.hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhh...eeeee..........---.....hhhhhhhhh..eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m22 A  42 PFPYAETDVADLQARMTAGELDSTTLTQAYLQRIAALDRTGPRLRAVIELNPDALKEAAERDRERRDGRLRGPLHGIPLLLKDNINAAPMATSAGSLALQGFRPDDAYLVRRLRDAGAVVLGKTNLSEWANFRGNDSISGWSARGGQTRNPYRISHSPCGSSSGSAVAVAANLASVAIGTETDGSIVCPAAINGVVGLKPTVGLVSRDGIIPISFSQDTAGPMARSVADAAAVLTAIAGRDDADPATATMPGRAVYDYTARLDPQGLRGKRIGLLQTPLLKYRGMPPLIEQAATELRRAGAVVVPVELPNQGAWAEAERTLLLYEFKAGLERYFNTHRAPLRSLADLIAFNQAHSKQELGLFGQELLVEADATAGLADPAYIRARSDARRLAGPEGIDAALAAHQLDALVAPTTGVAWPIRS---DFPGESYSAAAVAGYPSLTVPMGQIDGLPVGLLFMGTAWSEPKLIEMAYAYEQRTRARRPPHFDT 531
                                    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       391       401       411       421       431       441       451       461 |   | 471       481       491       501       511       521       531
                                                                                                                                                                                                                                                                                                                                                                                                                                                               463 467                                                                


Chain B from PDB  Type:PROTEIN  Length:487
 aligned with Q8RJN5_STEMA | Q8RJN5 from UniProtKB/TrEMBL  Length:540

    Alignment length:490
                                    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       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531
         Q8RJN5_STEMA    42 PFPYAETDVADLQARMTAGELDSTTLTQAYLQRIAALDRTGPRLRAVIELNPDALKEAAERDRERRDGRLRGPLHGIPLLLKDNINAAPMATSAGSLALQGFRPDDAYLVRRLRDAGAVVLGKTNLSEWANFRGNDSISGWSARGGQTRNPYRISHSPCGSSSGSAVAVAANLASVAIGTETDGSIVCPAAINGVVGLKPTVGLVSRDGIIPISFSQDTAGPMARSVADAAAVLTAIAGRDDADPATATMPGRAVYDYTARLDPQGLRGKRIGLLQTPLLKYRGMPPLIEQAATELRRAGAVVVPVELPNQGAWAEAERTLLLYEFKAGLERYFNTHRAPLRSLADLIAFNQAHSKQELGLFGQELLVEADATAGLADPAYIRARSDARRLAGPEGIDAALAAHQLDALVAPTTGVAWPIRSEGDDFPGESYSAAAVAGYPSLTVPMGQIDGLPVGLLFMGTAWSEPKLIEMAYAYEQRTRARRPPHFDT 531
               SCOP domains d1m22b_ B: Peptide amidase Pam                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1m22B00 B:42-531 Amidase signature (AS) enzymes                                                                                                                                                                                                                                                                                                                                                                                                                                                            CATH domains
           Pfam domains (1) ------------------------Amidase-1m22B01 B:66-511                                                                                                                                                                                                                                                                                                                                                                                                                                      -------------------- Pfam domains (1)
           Pfam domains (2) ------------------------Amidase-1m22B02 B:66-511                                                                                                                                                                                                                                                                                                                                                                                                                                      -------------------- Pfam domains (2)
         Sec.struct. author .......hhhhhhhhhhh...hhhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhh..........eeeee.............hhhhh......hhhhhhhhhh..eeeeee..hhhhhh........ee...ee..............hhhhhhhhhh....eeeeee....hhhhhhhh..eeee...................eeeeee.hhhhhhhhhhhhh.....hhhhhhh......hhhhhh........eeeee.hhhhhh.hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhh...eeeee..........---.....hhhhhhhhh..eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m22 B  42 PFPYAETDVADLQARMTAGELDSTTLTQAYLQRIAALDRTGPRLRAVIELNPDALKEAAERDRERRDGRLRGPLHGIPLLLKDNINAAPMATSAGSLALQGFRPDDAYLVRRLRDAGAVVLGKTNLSEWANFRGNDSISGWSARGGQTRNPYRISHSPCGSSSGSAVAVAANLASVAIGTETDGSIVCPAAINGVVGLKPTVGLVSRDGIIPISFSQDTAGPMARSVADAAAVLTAIAGRDDADPATATMPGRAVYDYTARLDPQGLRGKRIGLLQTPLLKYRGMPPLIEQAATELRRAGAVVVPVELPNQGAWAEAERTLLLYEFKAGLERYFNTHRAPLRSLADLIAFNQAHSKQELGLFGQELLVEADATAGLADPAYIRARSDARRLAGPEGIDAALAAHQLDALVAPTTGVAWPIRS---DFPGESYSAAAVAGYPSLTVPMGQIDGLPVGLLFMGTAWSEPKLIEMAYAYEQRTRARRPPHFDT 531
                                    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       391       401       411       421       431       441       451       461 |   | 471       481       491       501       511       521       531
                                                                                                                                                                                                                                                                                                                                                                                                                                                               463 467
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Amidase] (17)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8RJN5_STEMA | Q8RJN5)
molecular function
    GO:0016884    carbon-nitrogen ligase activity, with glutamine as amido-N-donor    Catalysis of the transfer of the amide nitrogen of glutamine to a variety of substrates. GATases catalyze two separate reactions at two active sites, which are located either on a single polypeptide chain or on different subunits. In the glutaminase reaction, glutamine is hydrolyzed to glutamate and ammonia, which is added to an acceptor substrate in the synthase reaction.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8RJN5_STEMA | Q8RJN5: 1m21 5ac3

(-) Related Entries Specified in the PDB File

1m21 1M21 CONTAINS THE PEPTIDE AMIDASE PAM COMPLEXED WITH THE COMPETITIVE INHIBITOR CHYMOSTATIN