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(-) Description

Title :  PANTOATE-BETA-ALANINE LIGASE FROM YERSINIA PESTIS IN COMPLEX WITH PANTOATE.
 
Authors :  J. Osipiuk, N. Maltseva, K. Kwon, W. F. Anderson, A. Joachimiak, Center Structural Genomics Of Infectious Diseases (Csgid)
Date :  16 Dec 10  (Deposition) - 02 Feb 11  (Release) - 02 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, N. Maltseva, K. Kwon, W. F. Anderson, A. Joachimiak
Pantoate-Beta-Alanine Ligase From Yersinia Pestis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PANTOATE--BETA-ALANINE LIGASE
    Chains: A, B, C, D
    EC Number: 6.3.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PANC, Y0785, YPO3402, YP_0283
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Strain: CO92
    Synonym: PANTOTHENATE SYNTHETASE, PS, 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2PAF4Ligand/IonPANTOATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PAF2Ligand/IonPANTOATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2PAF2Ligand/IonPANTOATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:28 , THR A:29 , GLN A:61 , ILE A:133 , GLN A:155 , HOH A:289 , HOH A:704 , HOH A:866 , HOH A:867BINDING SITE FOR RESIDUE PAF A 501
2AC2SOFTWAREGLN A:61 , ARG A:123 , HIS A:126 , ARG A:189BINDING SITE FOR RESIDUE CL A 285
3AC3SOFTWAREPRO B:28 , THR B:29 , GLN B:61 , ILE B:133 , GLN B:155 , HOH B:303 , HOH B:312BINDING SITE FOR RESIDUE PAF B 501
4AC4SOFTWAREPRO C:28 , THR C:29 , MET C:30 , GLN C:61 , ILE C:133 , GLN C:155 , HOH C:293 , HOH C:798 , HOH C:800BINDING SITE FOR RESIDUE PAF C 501
5AC5SOFTWAREGLN C:61 , ARG C:123 , HIS C:126 , ARG C:189 , HOH C:1028BINDING SITE FOR RESIDUE CL C 285
6AC6SOFTWAREPRO D:28 , THR D:29 , GLN D:61 , ILE D:133 , GLN D:155 , HOH D:782 , HOH D:811 , HOH D:812BINDING SITE FOR RESIDUE PAF D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q12)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q12)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q12)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q12)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q12)

(-) 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_YERPE | Q8ZBK7 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_YERPE     - -MLIIETLPLLRQQIRRWRQEGKRIALVPTMGNLHEGHMTLVDEAKTRADVVVVTIFVNPLQFERPDDLAHYPRTLQEDCEKLTRHGADLVFAPAAADIYPAGLEKQTYVDVPALSTILEGASRPGHFRGVSTIVSKLFNLIQPDVACFGEKDYQQLALIRKMVADMGYDINIVGVPTVRAKDGLALSSRNGYLTEEERQIAPQLSKIMWALAEKMALGERQIDALLEEAAAQLLRVGFTPDELFIRDAETLQPLTVDSQQAVILMAAWLGKARLIDNQLVDLRH 284
               SCOP domains d3q12a_ A: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh...eeeeee..hhhhh.hhhhhhhh..hhhhhhhhhhhh...eee..hhhhhh........eee.......hhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.ee...eeee............eeeeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q12 A   0 AMLIIETLPLLRQQIRRWRQEGKRIALVPTMGNLHEGHMTLVDEAKTRADVVVVTIFVNPLQFERPDDLAHYPRTLQEDCEKLTRHGADLVFAPAAADIYPAGLEKQTYVDVPALSTILEGASRPGHFRGVSTIVSKLFNLIQPDVACFGEKDYQQLALIRKMVADMGYDINIVGVPTVRAKDGLALSSRNGYLTEEERQIAPQLSKIMWALAEKMALGERQIDALLEEAAAQLLRVGFTPDELFIRDAETLQPLTVDSQQAVILMAAWLGKARLIDNQLVDLRH 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:284
 aligned with PANC_YERPE | Q8ZBK7 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_YERPE     - --MLIIETLPLLRQQIRRWRQEGKRIALVPTMGNLHEGHMTLVDEAKTRADVVVVTIFVNPLQFERPDDLAHYPRTLQEDCEKLTRHGADLVFAPAAADIYPAGLEKQTYVDVPALSTILEGASRPGHFRGVSTIVSKLFNLIQPDVACFGEKDYQQLALIRKMVADMGYDINIVGVPTVRAKDGLALSSRNGYLTEEERQIAPQLSKIMWALAEKMALGERQIDALLEEAAAQLLRVGFTPDELFIRDAETLQPLTVDSQQAVILMAAWLGKARLIDNQLVDL 282
               SCOP domains d3q12b_ B: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh...eeeeee..hhhhh..hhhhhh...hhhhhhhhhhhh...eee..hhhhhh........eee......hhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.ee...eeee............eeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q12 B  -1 NAMLIIETLPLLRQQIRRWRQEGKRIALVPTMGNLHEGHMTLVDEAKTRADVVVVTIFVNPLQFERPDDLAHYPRTLQEDCEKLTRHGADLVFAPAAADIYPAGLEKQTYVDVPALSTILEGASRPGHFRGVSTIVSKLFNLIQPDVACFGEKDYQQLALIRKMVADMGYDINIVGVPTVRAKDGLALSSRNGYLTEEERQIAPQLSKIMWALAEKMALGERQIDALLEEAAAQLLRVGFTPDELFIRDAETLQPLTVDSQQAVILMAAWLGKARLIDNQLVDL 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    


Chain C from PDB  Type:PROTEIN  Length:285
 aligned with PANC_YERPE | Q8ZBK7 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_YERPE     - -MLIIETLPLLRQQIRRWRQEGKRIALVPTMGNLHEGHMTLVDEAKTRADVVVVTIFVNPLQFERPDDLAHYPRTLQEDCEKLTRHGADLVFAPAAADIYPAGLEKQTYVDVPALSTILEGASRPGHFRGVSTIVSKLFNLIQPDVACFGEKDYQQLALIRKMVADMGYDINIVGVPTVRAKDGLALSSRNGYLTEEERQIAPQLSKIMWALAEKMALGERQIDALLEEAAAQLLRVGFTPDELFIRDAETLQPLTVDSQQAVILMAAWLGKARLIDNQLVDLRH 284
               SCOP domains d3q12c_ C: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh...eeeeee..hhhhh.hhhhhhhh..hhhhhhhhhhhh...eee..hhhhhh........eee.......hhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.ee...eeee............eeeeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q12 C   0 AMLIIETLPLLRQQIRRWRQEGKRIALVPTMGNLHEGHMTLVDEAKTRADVVVVTIFVNPLQFERPDDLAHYPRTLQEDCEKLTRHGADLVFAPAAADIYPAGLEKQTYVDVPALSTILEGASRPGHFRGVSTIVSKLFNLIQPDVACFGEKDYQQLALIRKMVADMGYDINIVGVPTVRAKDGLALSSRNGYLTEEERQIAPQLSKIMWALAEKMALGERQIDALLEEAAAQLLRVGFTPDELFIRDAETLQPLTVDSQQAVILMAAWLGKARLIDNQLVDLRH 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 D from PDB  Type:PROTEIN  Length:283
 aligned with PANC_YERPE | Q8ZBK7 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_YERPE     - -MLIIETLPLLRQQIRRWRQEGKRIALVPTMGNLHEGHMTLVDEAKTRADVVVVTIFVNPLQFERPDDLAHYPRTLQEDCEKLTRHGADLVFAPAAADIYPAGLEKQTYVDVPALSTILEGASRPGHFRGVSTIVSKLFNLIQPDVACFGEKDYQQLALIRKMVADMGYDINIVGVPTVRAKDGLALSSRNGYLTEEERQIAPQLSKIMWALAEKMALGERQIDALLEEAAAQLLRVGFTPDELFIRDAETLQPLTVDSQQAVILMAAWLGKARLIDNQLVDL 282
               SCOP domains d3q12d_ D: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Pantoate_ligase-3q12D01 D:1-280                                                                                                                                                                                                                                                         -- Pfam domains (1)
           Pfam domains (2) -Pantoate_ligase-3q12D02 D:1-280                                                                                                                                                                                                                                                         -- Pfam domains (2)
           Pfam domains (3) -Pantoate_ligase-3q12D03 D:1-280                                                                                                                                                                                                                                                         -- Pfam domains (3)
           Pfam domains (4) -Pantoate_ligase-3q12D04 D:1-280                                                                                                                                                                                                                                                         -- Pfam domains (4)
         Sec.struct. author ..eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh...eeeeee..hhhhh.hhhhhhhh..hhhhhhhhhhhh...eee..hhhhhh........eee......hhhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee..................hhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.ee...eeee............eeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q12 D   0 AMLIIETLPLLRQQIRRWRQEGKRIALVPTMGNLHEGHMTLVDEAKTRADVVVVTIFVNPLQFERPDDLAHYPRTLQEDCEKLTRHGADLVFAPAAADIYPAGLEKQTYVDVPALSTILEGASRPGHFRGVSTIVSKLFNLIQPDVACFGEKDYQQLALIRKMVADMGYDINIVGVPTVRAKDGLALSSRNGYLTEEERQIAPQLSKIMWALAEKMALGERQIDALLEEAAAQLLRVGFTPDELFIRDAETLQPLTVDSQQAVILMAAWLGKARLIDNQLVDL 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
   Legend:   → Mismatch (orange background)
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    → 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 3Q12)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PANC_YERPE | Q8ZBK7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        PANC_YERPE | Q8ZBK7: 3q10

(-) Related Entries Specified in the PDB File

3q10 PANTOATE-BETA-ALANINE LIGASE FROM YERSINIA PESTIS IN COMPLEX WITH AMP. RELATED ID: IDP90523 RELATED DB: TARGETDB