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(-) Description

Title :  MCSG APC5046 PROBABLE GLUTAMINASE YBAS
 
Authors :  C. Chang, M. E. Cuff, A. Joachimiak, A. Savchenko, A. Edwards, T. Skarin Center For Structural Genomics (Mcsg)
Date :  28 Jul 04  (Deposition) - 07 Sep 04  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (1x),B (1x),C (1x),D (1x)
Biol. Unit 4:  A (1x),B (1x),C (1x),D (1x)
Keywords :  Structural Genomics, Apc5046, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Brown, A. Singer, M. Proudfoot, T. Skarina, Y. Kim, C. Chang, I. Dementieva, E. Kuznetsova, C. F. Gonzalez, A. Joachimiak, A. Savchenko, A. F. Yakunin
Functional And Structural Characterization Of Four Glutaminases From Escherichia Coli And Bacillus Subtilis.
Biochemistry V. 47 5724 2008
PubMed-ID: 18459799  |  Reference-DOI: 10.1021/BI800097H

(-) Compounds

Molecule 1 - PROBABLE GLUTAMINASE YBAS
    Chains: A, B, C, D
    EC Number: 3.5.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YBAS
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (1x): A (1x)B (1x)C (1x)D (1x)
Biological Unit 4 (1x): A (1x)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric Unit (2, 21)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL
2FMT9Ligand/IonFORMIC ACID
Biological Unit 1 (2, 14)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2FMT6Ligand/IonFORMIC ACID
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2FMT3Ligand/IonFORMIC ACID
Biological Unit 3 (2, 14)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2FMT6Ligand/IonFORMIC ACID
Biological Unit 4 (2, 14)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2FMT6Ligand/IonFORMIC ACID

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:294 , HOH A:1377 , THR B:16 , GLN B:17BINDING SITE FOR RESIDUE EDO A 1203
02AC2SOFTWARELYS A:88 , GLY A:179 , TYR A:180 , EDO A:1205 , HOH A:1527BINDING SITE FOR RESIDUE EDO A 1204
03AC3SOFTWAREASP A:87 , LYS A:88 , EDO A:1204BINDING SITE FOR RESIDUE EDO A 1205
04AC4SOFTWAREPHE A:98 , GLY A:287 , FMT A:1212 , HOH A:1413 , HOH A:1415BINDING SITE FOR RESIDUE EDO A 1211
05AC5SOFTWAREASP A:59 , ASN A:201 , HOH A:1229 , HOH A:1285 , HOH A:1374BINDING SITE FOR RESIDUE EDO A 1217
06AC6SOFTWAREPRO A:37 , GLN A:39 , LEU A:40 , HOH A:1380 , HOH A:1462 , HOH A:1489 , HIS D:222 , HOH D:1312BINDING SITE FOR RESIDUE EDO A 1219
07AC7SOFTWAREASN B:128 , ARG B:138BINDING SITE FOR RESIDUE EDO B 1210
08AC8SOFTWAREGLU B:65 , GLU B:161 , ASN B:168 , TYR B:192 , THR B:193 , HOH B:1288 , HOH B:1404 , HOH B:1413BINDING SITE FOR RESIDUE EDO B 1224
09AC9SOFTWAREVAL C:52 , ARG C:224 , GLN C:227 , HOH C:1284 , HOH C:1298 , HOH C:1316 , HOH C:1382BINDING SITE FOR RESIDUE EDO C 1208
10BC1SOFTWAREGLU D:65 , GLU D:161 , ASN D:168 , THR D:193 , CYS D:196 , HOH D:1249 , HOH D:1293 , HOH D:1372BINDING SITE FOR RESIDUE EDO D 1213
11BC2SOFTWAREGLY D:287 , FMT D:1215 , HOH D:1418 , HOH D:1436 , HOH D:1486BINDING SITE FOR RESIDUE EDO D 1214
12BC3SOFTWAREGLN D:25 , ASN D:26BINDING SITE FOR RESIDUE EDO D 1216
13BC4SOFTWAREGLN A:25 , ASP A:284 , EDO A:1211 , HOH A:1433BINDING SITE FOR RESIDUE FMT A 1212
14BC5SOFTWARELEU A:199 , HOH A:1278 , HOH A:1347 , HOH A:1372BINDING SITE FOR RESIDUE FMT A 1218
15BC6SOFTWAREGLN B:39 , ALA B:178 , FMT B:1207BINDING SITE FOR RESIDUE FMT B 1206
16BC7SOFTWAREGLN B:39 , GLY B:179 , TYR B:180 , TYR B:182 , FMT B:1206 , HOH B:1410 , HOH B:1444BINDING SITE FOR RESIDUE FMT B 1207
17BC8SOFTWARESER B:100 , VAL B:101 , ILE B:102 , HOH B:1460 , GLU C:105 , HOH C:1430BINDING SITE FOR RESIDUE FMT B 1209
18BC9SOFTWAREASN B:22 , GLY B:23 , GLY B:24BINDING SITE FOR RESIDUE FMT B 1225
19CC1SOFTWAREASN C:51 , VAL C:52 , GLU C:78 , HOH C:1427BINDING SITE FOR RESIDUE FMT C 1222
20CC2SOFTWAREASN C:22 , GLY C:23 , ARG C:291BINDING SITE FOR RESIDUE FMT C 1226
21CC3SOFTWARESER D:66 , TYR D:244 , VAL D:262 , EDO D:1214 , HOH D:1224 , HOH D:1242 , HOH D:1361BINDING SITE FOR RESIDUE FMT D 1215

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U60)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U60)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U60)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U60)

(-) Exons   (0, 0)

(no "Exon" information available for 1U60)

(-) 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:309
 aligned with GLSA1_ECOLI | P77454 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:309
                                    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         
          GLSA1_ECOLI     2 LDANKLQQAVDQAYTQFHSLNGGQNADYIPFLANVPGQLAAVAIVTCDGNVYSAGDSDYRFALESISKVCTLALALEDVGPQAVQDKIGADPTGLPFNSVIALELHGGKPLSPLVNAGAIATTSLINAENVEQRWQRILHIQQQLAGEQVALSDEVNQSEQTTNFHNRAIAWLLYSAGYLYCDAMEACDVYTRQCSTLLNTIELATLGATLAAGGVNPLTHKRVLQADNVPYILAEMMMEGLYGRSGDWAYRVGLPGKSGVGGGILAVVPGVMGIAAFSPPLDEDGNSVRGQKMVASVAKQLGYNVFKG 310
               SCOP domains d1u60a_ A: Probable glutaminase YbaS                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1u60A00 A:2-310 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..........hhhhhh......eeeeee....eeeee.....ee...hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhh.eeehhhhhhhhhhhhhh..ee....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeeeee...eeeeee.........hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u60 A   2 LDANKLQQAVDQAYTQFHSLNGGQNADYIPFLANVPGQLAAVAIVTCDGNVYSAGDSDYRFALESISKVCTLALALEDVGPQAVQDKIGADPTGLPFNSVIALELHGGKPLSPLVNAGAIATTSLINAENVEQRWQRILHIQQQLAGEQVALSDEVNQSEQTTNFHNRAIAWLLYSAGYLYCDAMEACDVYTRQCSTLLNTIELATLGATLAAGGVNPLTHKRVLQADNVPYILAEMMMEGLYGRSGDWAYRVGLPGKSGVGGGILAVVPGVMGIAAFSPPLDEDGNSVRGQKMVASVAKQLGYNVFKG 310
                                    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:309
 aligned with GLSA1_ECOLI | P77454 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:309
                                    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         
          GLSA1_ECOLI     2 LDANKLQQAVDQAYTQFHSLNGGQNADYIPFLANVPGQLAAVAIVTCDGNVYSAGDSDYRFALESISKVCTLALALEDVGPQAVQDKIGADPTGLPFNSVIALELHGGKPLSPLVNAGAIATTSLINAENVEQRWQRILHIQQQLAGEQVALSDEVNQSEQTTNFHNRAIAWLLYSAGYLYCDAMEACDVYTRQCSTLLNTIELATLGATLAAGGVNPLTHKRVLQADNVPYILAEMMMEGLYGRSGDWAYRVGLPGKSGVGGGILAVVPGVMGIAAFSPPLDEDGNSVRGQKMVASVAKQLGYNVFKG 310
               SCOP domains d1u60b_ B: Probable glutaminase YbaS                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1u60B00 B:2-310 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..........hhhhhh......eeeeee....eeeee.....ee...hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhh.........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhh.eeehhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeeeee...eeeeee.........hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u60 B   2 LDANKLQQAVDQAYTQFHSLNGGQNADYIPFLANVPGQLAAVAIVTCDGNVYSAGDSDYRFALESISKVCTLALALEDVGPQAVQDKIGADPTGLPFNSVIALELHGGKPLSPLVNAGAIATTSLINAENVEQRWQRILHIQQQLAGEQVALSDEVNQSEQTTNFHNRAIAWLLYSAGYLYCDAMEACDVYTRQCSTLLNTIELATLGATLAAGGVNPLTHKRVLQADNVPYILAEMMMEGLYGRSGDWAYRVGLPGKSGVGGGILAVVPGVMGIAAFSPPLDEDGNSVRGQKMVASVAKQLGYNVFKG 310
                                    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:309
 aligned with GLSA1_ECOLI | P77454 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:309
                                    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         
          GLSA1_ECOLI     2 LDANKLQQAVDQAYTQFHSLNGGQNADYIPFLANVPGQLAAVAIVTCDGNVYSAGDSDYRFALESISKVCTLALALEDVGPQAVQDKIGADPTGLPFNSVIALELHGGKPLSPLVNAGAIATTSLINAENVEQRWQRILHIQQQLAGEQVALSDEVNQSEQTTNFHNRAIAWLLYSAGYLYCDAMEACDVYTRQCSTLLNTIELATLGATLAAGGVNPLTHKRVLQADNVPYILAEMMMEGLYGRSGDWAYRVGLPGKSGVGGGILAVVPGVMGIAAFSPPLDEDGNSVRGQKMVASVAKQLGYNVFKG 310
               SCOP domains d1u60c_ C: Probable glutaminase YbaS                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1u60C00 C:2-310 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..........hhhhhh......eeeeee....eeeee.....ee...hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhh.........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhheeehhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeeeee...eeeeee.........hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u60 C   2 LDANKLQQAVDQAYTQFHSLNGGQNADYIPFLANVPGQLAAVAIVTCDGNVYSAGDSDYRFALESISKVCTLALALEDVGPQAVQDKIGADPTGLPFNSVIALELHGGKPLSPLVNAGAIATTSLINAENVEQRWQRILHIQQQLAGEQVALSDEVNQSEQTTNFHNRAIAWLLYSAGYLYCDAMEACDVYTRQCSTLLNTIELATLGATLAAGGVNPLTHKRVLQADNVPYILAEMMMEGLYGRSGDWAYRVGLPGKSGVGGGILAVVPGVMGIAAFSPPLDEDGNSVRGQKMVASVAKQLGYNVFKG 310
                                    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:309
 aligned with GLSA1_ECOLI | P77454 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:309
                                    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         
          GLSA1_ECOLI     2 LDANKLQQAVDQAYTQFHSLNGGQNADYIPFLANVPGQLAAVAIVTCDGNVYSAGDSDYRFALESISKVCTLALALEDVGPQAVQDKIGADPTGLPFNSVIALELHGGKPLSPLVNAGAIATTSLINAENVEQRWQRILHIQQQLAGEQVALSDEVNQSEQTTNFHNRAIAWLLYSAGYLYCDAMEACDVYTRQCSTLLNTIELATLGATLAAGGVNPLTHKRVLQADNVPYILAEMMMEGLYGRSGDWAYRVGLPGKSGVGGGILAVVPGVMGIAAFSPPLDEDGNSVRGQKMVASVAKQLGYNVFKG 310
               SCOP domains d1u60d_ D: Probable glutaminase YbaS                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1u60D00 D:2-310 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) ----------------------Glutaminase-1u60D01 D:24-308                                                                                                                                                                                                                                                                 -- Pfam domains (1)
           Pfam domains (2) ----------------------Glutaminase-1u60D02 D:24-308                                                                                                                                                                                                                                                                 -- Pfam domains (2)
           Pfam domains (3) ----------------------Glutaminase-1u60D03 D:24-308                                                                                                                                                                                                                                                                 -- Pfam domains (3)
           Pfam domains (4) ----------------------Glutaminase-1u60D04 D:24-308                                                                                                                                                                                                                                                                 -- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhh..........hhhhhh......eeeeee....eeeee.....ee...hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhheeehhhhhhhhhhhhhh..ee....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeeeee...eeeeee.........hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u60 D   2 LDANKLQQAVDQAYTQFHSLNGGQNADYIPFLANVPGQLAAVAIVTCDGNVYSAGDSDYRFALESISKVCTLALALEDVGPQAVQDKIGADPTGLPFNSVIALELHGGKPLSPLVNAGAIATTSLINAENVEQRWQRILHIQQQLAGEQVALSDEVNQSEQTTNFHNRAIAWLLYSAGYLYCDAMEACDVYTRQCSTLLNTIELATLGATLAAGGVNPLTHKRVLQADNVPYILAEMMMEGLYGRSGDWAYRVGLPGKSGVGGGILAVVPGVMGIAAFSPPLDEDGNSVRGQKMVASVAKQLGYNVFKG 310
                                    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: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Beta-lactamase (210)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (GLSA1_ECOLI | P77454)
molecular function
    GO:0004359    glutaminase activity    Catalysis of the reaction: L-glutamine + H2O = L-glutamate + NH3.
    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.
biological process
    GO:0006537    glutamate biosynthetic process    The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid.
    GO:0006543    glutamine catabolic process    The chemical reactions and pathways resulting in the breakdown of glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0045926    negative regulation of growth    Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism.
    GO:0010447    response to acidic pH    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution.

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  1u60
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