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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE PEPTIDE AMIDASE PAM IN COMPLEX WITH THE COMPETITIVE INHIBITOR CHYMOSTATIN
 
Authors :  J. Labahn, S. Neumann, G. Buldt, M. -R. Kula, J. Granzin
Date :  21 Jun 02  (Deposition) - 16 Oct 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Protein-Inhibitor Complex, Core: Eleven-Stranded Beta-Sheet, Covered: Double Layers Of Alpha Helices On Top And Bottom, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (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
 
Molecule 2 - CHYMOSTATIN
    Chains: C, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CSI2Mod. Amino AcidAMINO-(2-IMINO-HEXAHYDRO-PYRIMIDIN-4-YL)-ACETIC ACID
2PHA2Mod. Amino AcidPHENYLALANINAL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CSI1Mod. Amino AcidAMINO-(2-IMINO-HEXAHYDRO-PYRIMIDIN-4-YL)-ACETIC ACID
2PHA1Mod. Amino AcidPHENYLALANINAL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CSI1Mod. Amino AcidAMINO-(2-IMINO-HEXAHYDRO-PYRIMIDIN-4-YL)-ACETIC ACID
2PHA1Mod. Amino AcidPHENYLALANINAL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:171 , ASN A:172 , PHE A:173 , SER A:180 , CYS A:200 , GLY A:201 , SER A:202 , ASP A:224 , SER A:226 , CYS A:229 , ILE A:254 , ARG A:360 , LEU A:363 , LEU A:407 , PHE A:468 , TYR A:473 , HOH A:902 , HOH A:933BINDING SITE FOR CHAIN C OF CHYMOSTATIN
2AC2SOFTWAREALA B:171 , ASN B:172 , PHE B:173 , SER B:180 , CYS B:200 , GLY B:201 , SER B:202 , ASP B:224 , SER B:226 , CYS B:229 , ILE B:254 , ARG B:360 , LEU B:363 , LEU B:407 , PHE B:468 , TYR B:473 , HOH B:1937BINDING SITE FOR CHAIN D OF CHYMOSTATIN

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M21)

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M21)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M21)

(-) Exons   (0, 0)

(no "Exon" information available for 1M21)

(-) 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:487
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       
         Q8RJN5_STEMA    43 FPYAETDVADLQARMTAGELDSTTLTQAYLQRIAALDRTGPRLRAVIELNPDALKEAAERDRERRDGRLRGPLHGIPLLLKDNINAAPMATSAGSLALQGFRPDDAYLVRRLRDAGAVVLGKTNLSEWANFRGNDSISGWSARGGQTRNPYRISHSPCGSSSGSAVAVAANLASVAIGTETDGSIVCPAAINGVVGLKPTVGLVSRDGIIPISFSQDTAGPMARSVADAAAVLTAIAGRDDADPATATMPGRAVYDYTARLDPQGLRGKRIGLLQTPLLKYRGMPPLIEQAATELRRAGAVVVPVELPNQGAWAEAERTLLLYEFKAGLERYFNTHRAPLRSLADLIAFNQAHSKQELGLFGQELLVEADATAGLADPAYIRARSDARRLAGPEGIDAALAAHQLDALVAPTTGVAWPIRSEGDDFPGESYSAAAVAGYPSLTVPMGQIDGLPVGLLFMGTAWSEPKLIEMAYAYEQRTRARRPPHF 529
               SCOP domains d1m21a_ A: Peptide amidase Pam                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1m21A00 A:43-529 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...................hhhhhhhh..eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m21 A  43 FPYAETDVADLQARMTAGELDSTTLTQAYLQRIAALDRTGPRLRAVIELNPDALKEAAERDRERRDGRLRGPLHGIPLLLKDNINAAPMATSAGSLALQGFRPDDAYLVRRLRDAGAVVLGKTNLSEWANFRGNDSISGWSARGGQTRNPYRISHSPCGSSSGSAVAVAANLASVAIGTETDGSIVCPAAINGVVGLKPTVGLVSRDGIIPISFSQDTAGPMARSVADAAAVLTAIAGRDDADPATATMPGRAVYDYTARLDPQGLRGKRIGLLQTPLLKYRGMPPLIEQAATELRRAGAVVVPVELPNQGAWAEAERTLLLYEFKAGLERYFNTHRAPLRSLADLIAFNQAHSKQELGLFGQELLVEADATAGLADPAYIRARSDARRLAGPEGIDAALAAHQLDALVAPTTGVAWPIRSEGDDFPGESYSAAAVAGYPSLTVPMGQIDGLPVGLLFMGTAWSEPKLIEMAYAYEQRTRARRPPHF 529
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       


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

    Alignment length:487
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       
         Q8RJN5_STEMA    43 FPYAETDVADLQARMTAGELDSTTLTQAYLQRIAALDRTGPRLRAVIELNPDALKEAAERDRERRDGRLRGPLHGIPLLLKDNINAAPMATSAGSLALQGFRPDDAYLVRRLRDAGAVVLGKTNLSEWANFRGNDSISGWSARGGQTRNPYRISHSPCGSSSGSAVAVAANLASVAIGTETDGSIVCPAAINGVVGLKPTVGLVSRDGIIPISFSQDTAGPMARSVADAAAVLTAIAGRDDADPATATMPGRAVYDYTARLDPQGLRGKRIGLLQTPLLKYRGMPPLIEQAATELRRAGAVVVPVELPNQGAWAEAERTLLLYEFKAGLERYFNTHRAPLRSLADLIAFNQAHSKQELGLFGQELLVEADATAGLADPAYIRARSDARRLAGPEGIDAALAAHQLDALVAPTTGVAWPIRSEGDDFPGESYSAAAVAGYPSLTVPMGQIDGLPVGLLFMGTAWSEPKLIEMAYAYEQRTRARRPPHF 529
               SCOP domains d1m21b_ B: Peptide amidase Pam                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1m21B00 B:43-529 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...................hhhhhhhh..eeeeeeeee..eeeeeeee....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m21 B  43 FPYAETDVADLQARMTAGELDSTTLTQAYLQRIAALDRTGPRLRAVIELNPDALKEAAERDRERRDGRLRGPLHGIPLLLKDNINAAPMATSAGSLALQGFRPDDAYLVRRLRDAGAVVLGKTNLSEWANFRGNDSISGWSARGGQTRNPYRISHSPCGSSSGSAVAVAANLASVAIGTETDGSIVCPAAINGVVGLKPTVGLVSRDGIIPISFSQDTAGPMARSVADAAAVLTAIAGRDDADPATATMPGRAVYDYTARLDPQGLRGKRIGLLQTPLLKYRGMPPLIEQAATELRRAGAVVVPVELPNQGAWAEAERTLLLYEFKAGLERYFNTHRAPLRSLADLIAFNQAHSKQELGLFGQELLVEADATAGLADPAYIRARSDARRLAGPEGIDAALAAHQLDALVAPTTGVAWPIRSEGDDFPGESYSAAAVAGYPSLTVPMGQIDGLPVGLLFMGTAWSEPKLIEMAYAYEQRTRARRPPHF 529
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       


Chain C from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 1m21 C   1 FxLf   4
                             | |
                             2-CSI
                               4-PHA


Chain D from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 1m21 D   1 FxLf   4
                             | |
                             | |
                             2-CSI
                               4-PHA
   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  (0, 0)

(no "Pfam Domain" information available for 1M21)

(-) 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: 1m22 5ac3

(-) Related Entries Specified in the PDB File

1m22 1M22 CONTAINS NATIVE PEPTIDE AMIDASE AT 1.4 A