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(-) Description

Title :  CRYSTAL STRUCTURE OF PANTOATE-BETA-ALANINE LIGASE FROM SALMONELLA TYPHIMURIUM
 
Authors :  Y. Kim, M. Makowska-Grzyska, N. Maltseva, K. Kwon, W. F. Anderson, A. Jo
Date :  03 May 10  (Deposition) - 26 May 10  (Release) - 26 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Alpha-Beta Fold, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kim, M. Makowska-Grzyska, N. Maltseva, K. Kwon, W. F. Anderson, A. Joachimiak
Crystal Structure Of Pantoate-Beta-Alanine Ligase From Salmonella Typhimurium
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PANTOTHENATE SYNTHETASE
    ChainsA, B, C, D
    EC Number6.3.2.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System StrainBL21MAGIC
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GenePANC
    Organism ScientificSALMONELLA TYPHIMURIUM
    Organism Taxid99287
    StrainLT2
    SynonymPS, PANTOATE--BETA-ALANINE LIGASE, PANTOATE-ACTIVATING ENZYME

 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  (4, 24)

Asymmetric Unit (4, 24)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2EOH5Ligand/IonETHANOL
3GOL16Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (4, 15)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2EOH4Ligand/IonETHANOL
3GOL8Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1ACY-1Ligand/IonACETIC ACID
2EOH1Ligand/IonETHANOL
3GOL8Ligand/IonGLYCEROL
4SO4-1Ligand/IonSULFATE ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:28 , GLN A:61 , ILE A:133 , GLN A:155 , HOH A:354BINDING SITE FOR RESIDUE GOL A 291
02AC2SOFTWAREHIS A:34BINDING SITE FOR RESIDUE EOH A 292
03AC3SOFTWAREGLN A:142 , PRO A:143 , ASP A:169 , GLN B:142BINDING SITE FOR RESIDUE SO4 A 293
04AC4SOFTWAREARG A:160 , ILE A:172BINDING SITE FOR RESIDUE GOL A 294
05AC5SOFTWAREASN A:206 , GLU A:232 , LYS A:236 , GLU B:77 , GLU B:80BINDING SITE FOR RESIDUE ACY A 295
06AC6SOFTWAREILE A:226 , ILE A:245 , GLU A:253BINDING SITE FOR RESIDUE EOH A 296
07AC7SOFTWAREGLU A:5 , ALA A:92 , GLN C:271BINDING SITE FOR RESIDUE SO4 A 297
08AC8SOFTWAREMET A:30 , GLN A:61 , PHE A:62 , ARG A:123 , HIS A:126BINDING SITE FOR RESIDUE EOH A 298
09AC9SOFTWARELYS A:214 , HIS B:34 , ASP B:35 , LEU B:68 , LEU B:186 , HOH B:356BINDING SITE FOR RESIDUE GOL B 291
10BC1SOFTWAREPRO B:28 , MET B:30 , GLN B:61 , ILE B:133 , GLN B:155 , HOH B:330BINDING SITE FOR RESIDUE GOL B 292
11BC2SOFTWAREASN B:32 , ARG B:73 , HOH B:328BINDING SITE FOR RESIDUE GOL B 293
12BC3SOFTWARELYS A:161 , ASP A:165 , TYR B:99 , PRO B:100 , HIS B:101 , GLY B:102 , GLY B:105 , GLN B:106BINDING SITE FOR RESIDUE GOL B 294
13BC4SOFTWARESER B:115 , GLY B:120 , ARG B:123 , PRO B:124 , GLY B:125 , HIS B:126 , PHE B:127 , ARG B:128 , HOH B:340 , HOH B:352 , HOH B:373BINDING SITE FOR RESIDUE GOL B 295
14BC5SOFTWAREGLN B:244 , ILE B:245 , ARG B:246 , LYS D:22BINDING SITE FOR RESIDUE GOL B 296
15BC6SOFTWAREARG B:18 , PRO B:143 , ASP B:169BINDING SITE FOR RESIDUE EOH B 297
16BC7SOFTWAREPRO C:28 , GLN C:61 , ILE C:133 , GLN C:155 , HOH C:318BINDING SITE FOR RESIDUE GOL C 292
17BC8SOFTWAREMET C:30 , GLN C:61 , PHE C:62 , ARG C:123 , HIS C:126BINDING SITE FOR RESIDUE GOL C 293
18BC9SOFTWAREGLU C:119 , PHE C:127 , ASP C:152 , PHE C:153 , GLN C:154 , GLN C:155BINDING SITE FOR RESIDUE GOL C 294
19CC1SOFTWAREHOH C:324BINDING SITE FOR RESIDUE EOH C 295
20CC2SOFTWAREGLN B:19 , ALA C:180 , TYR C:205BINDING SITE FOR RESIDUE GOL C 296
21CC3SOFTWAREARG C:18 , GLN C:142 , PRO C:143 , ASP C:169 , ARG D:18 , GLN D:142BINDING SITE FOR RESIDUE GOL D 291
22CC4SOFTWAREGLN C:142 , GLN D:142 , PRO D:143 , ASP D:169 , ILE D:170 , HOH D:297BINDING SITE FOR RESIDUE GOL D 285
23CC5SOFTWARELYS C:161 , ASP C:165 , HIS D:101 , GLY D:102 , GLY D:105 , GLN D:106BINDING SITE FOR RESIDUE GOL D 292
24CC6SOFTWAREGLN D:61 , GLN D:155 , HOH D:332BINDING SITE FOR RESIDUE GOL D 293

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MUE)

(-) 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:285
 aligned with PANC_SALTY | Q8ZRR1 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:285
                             1                                                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279     
           PANC_SALTY     - -MLIIETLPLLRQHIRRLRQEGKRVALVPTMGNLHDGHMKLVDEAKARADVVIVSIFVNPMQFDRPDDLVRYPRTLQEDCEKLNKRKVDYVFAPAVEEIYPHGLEGQTYVDVPGLSTMLEGASRPGHFRGVSTIVSKLFNLIQPDIACFGEKDFQQLALIRKMVADMSYDIEIVGVPIIRAKDGLALSSRNAYLTAEQRKIAPGLYNVMNSIAEKLIAGNRELQEIIAIAEQELNEKGFRADDIQIRDADTLLELTETSKRAVILAAAWLGQARLIDNQSVTLAQ 284
               SCOP domains d3muea_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh.eeeeee..hhhhh.hhhhhhh...hhhhhhhhhhhh...eee..hhhhhh........eee......hhhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee............hhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.eeeeeeeee............eeeeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mue A   0 AMLIIETLPLLRQHIRRLRQEGKRVALVPTMGNLHDGHMKLVDEAKARADVVIVSIFVNPMQFDRPDDLVRYPRTLQEDCEKLNKRKVDYVFAPAVEEIYPHGLEGQTYVDVPGLSTMLEGASRPGHFRGVSTIVSKLFNLIQPDIACFGEKDFQQLALIRKMVADMSYDIEIVGVPIIRAKDGLALSSRNAYLTAEQRKIAPGLYNVMNSIAEKLIAGNRELQEIIAIAEQELNEKGFRADDIQIRDADTLLELTETSKRAVILAAAWLGQARLIDNQSVTLAQ 284
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279     

Chain B from PDB  Type:PROTEIN  Length:285
 aligned with PANC_SALTY | Q8ZRR1 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:285
                              1                                                                                                                                                                                                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278     
           PANC_SALTY     - --MLIIETLPLLRQHIRRLRQEGKRVALVPTMGNLHDGHMKLVDEAKARADVVIVSIFVNPMQFDRPDDLVRYPRTLQEDCEKLNKRKVDYVFAPAVEEIYPHGLEGQTYVDVPGLSTMLEGASRPGHFRGVSTIVSKLFNLIQPDIACFGEKDFQQLALIRKMVADMSYDIEIVGVPIIRAKDGLALSSRNAYLTAEQRKIAPGLYNVMNSIAEKLIAGNRELQEIIAIAEQELNEKGFRADDIQIRDADTLLELTETSKRAVILAAAWLGQARLIDNQSVTLA 283
               SCOP domains d3mueb_ B: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh...eeeeee..................hhhhhhhhhhhh...eee..hhhhhh........eee......hhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeeeeeeee............eeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mue B  -1 NAMLIIETLPLLRQHIRRLRQEGKRVALVPTMGNLHDGHMKLVDEAKARADVVIVSIFVNPMQFDRPDDLVRYPRTLQEDCEKLNKRKVDYVFAPAVEEIYPHGLEGQTYVDVPGLSTMLEGASRPGHFRGVSTIVSKLFNLIQPDIACFGEKDFQQLALIRKMVADMSYDIEIVGVPIIRAKDGLALSSRNAYLTAEQRKIAPGLYNVMNSIAEKLIAGNRELQEIIAIAEQELNEKGFRADDIQIRDADTLLELTETSKRAVILAAAWLGQARLIDNQSVTLA 283
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278     

Chain C from PDB  Type:PROTEIN  Length:283
 aligned with PANC_SALTY | Q8ZRR1 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:283
                             1                                                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279   
           PANC_SALTY     - -MLIIETLPLLRQHIRRLRQEGKRVALVPTMGNLHDGHMKLVDEAKARADVVIVSIFVNPMQFDRPDDLVRYPRTLQEDCEKLNKRKVDYVFAPAVEEIYPHGLEGQTYVDVPGLSTMLEGASRPGHFRGVSTIVSKLFNLIQPDIACFGEKDFQQLALIRKMVADMSYDIEIVGVPIIRAKDGLALSSRNAYLTAEQRKIAPGLYNVMNSIAEKLIAGNRELQEIIAIAEQELNEKGFRADDIQIRDADTLLELTETSKRAVILAAAWLGQARLIDNQSVTL 282
               SCOP domains d3muec_ C: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh.eeeeee..hhhhh.hhhhhh....hhhhhhhhhhhh...eee..hhhhhh........eee......hhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeeeeeeee............eeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mue C   0 AMLIIETLPLLRQHIRRLRQEGKRVALVPTMGNLHDGHMKLVDEAKARADVVIVSIFVNPMQFDRPDDLVRYPRTLQEDCEKLNKRKVDYVFAPAVEEIYPHGLEGQTYVDVPGLSTMLEGASRPGHFRGVSTIVSKLFNLIQPDIACFGEKDFQQLALIRKMVADMSYDIEIVGVPIIRAKDGLALSSRNAYLTAEQRKIAPGLYNVMNSIAEKLIAGNRELQEIIAIAEQELNEKGFRADDIQIRDADTLLELTETSKRAVILAAAWLGQARLIDNQSVTL 282
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279   

Chain D from PDB  Type:PROTEIN  Length:284
 aligned with PANC_SALTY | Q8ZRR1 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:284
                              1                                                                                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278    
           PANC_SALTY     - --MLIIETLPLLRQHIRRLRQEGKRVALVPTMGNLHDGHMKLVDEAKARADVVIVSIFVNPMQFDRPDDLVRYPRTLQEDCEKLNKRKVDYVFAPAVEEIYPHGLEGQTYVDVPGLSTMLEGASRPGHFRGVSTIVSKLFNLIQPDIACFGEKDFQQLALIRKMVADMSYDIEIVGVPIIRAKDGLALSSRNAYLTAEQRKIAPGLYNVMNSIAEKLIAGNRELQEIIAIAEQELNEKGFRADDIQIRDADTLLELTETSKRAVILAAAWLGQARLIDNQSVTL 282
               SCOP domains d3mued_ D: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Pantoate_ligase-3mueD01 D:1-280                                                                                                                                                                                                                                                         -- Pfam domains (1)
           Pfam domains (2) --Pantoate_ligase-3mueD02 D:1-280                                                                                                                                                                                                                                                         -- Pfam domains (2)
           Pfam domains (3) --Pantoate_ligase-3mueD03 D:1-280                                                                                                                                                                                                                                                         -- Pfam domains (3)
           Pfam domains (4) --Pantoate_ligase-3mueD04 D:1-280                                                                                                                                                                                                                                                         -- Pfam domains (4)
         Sec.struct. author ...eee.hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhh.eeeeee..hhhhh.hhhhhhhh..hhhhhhhhhhh....eee..hhhhhh........eee......hhhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeeeeeeee............eeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mue D  -1 NAMLIIETLPLLRQHIRRLRQEGKRVALVPTMGNLHDGHMKLVDEAKARADVVIVSIFVNPMQFDRPDDLVRYPRTLQEDCEKLNKRKVDYVFAPAVEEIYPHGLEGQTYVDVPGLSTMLEGASRPGHFRGVSTIVSKLFNLIQPDIACFGEKDFQQLALIRKMVADMSYDIEIVGVPIIRAKDGLALSSRNAYLTAEQRKIAPGLYNVMNSIAEKLIAGNRELQEIIAIAEQELNEKGFRADDIQIRDADTLLELTETSKRAVILAAAWLGQARLIDNQSVTL 282
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278    

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PANC_SALTY | Q8ZRR1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004592    pantoate-beta-alanine ligase activity    Catalysis of the reaction: ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0015940    pantothenate biosynthetic process    The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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