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(-) Description

Title :  PANTOATE-BETA-ALANINE LIGASE FROM YERSINIA PESTIS
 
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 :  1.83
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,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): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1AMP4Ligand/IonADENOSINE MONOPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3GOL5Ligand/IonGLYCEROL
4IMD1Ligand/IonIMIDAZOLE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4IMD1Ligand/IonIMIDAZOLE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4IMD-1Ligand/IonIMIDAZOLE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:28 , MET A:30 , HIS A:34 , HIS A:37 , LEU A:40 , PHE A:148 , GLY A:149 , ASP A:152 , PRO A:176 , THR A:177 , VAL A:178 , LEU A:186 , HOH A:358 , HOH A:376 , HOH A:386 , HOH A:414 , HOH A:417 , HOH A:436 , GOL A:601 , HOH A:615BINDING SITE FOR RESIDUE AMP A 501
02AC2SOFTWAREPRO B:28 , MET B:30 , HIS B:34 , HIS B:37 , LEU B:40 , PHE B:148 , GLY B:149 , ASP B:152 , PRO B:176 , THR B:177 , VAL B:178 , LEU B:186 , HOH B:285 , HOH B:311 , HOH B:338 , HOH B:340 , HOH B:362 , GOL B:603BINDING SITE FOR RESIDUE AMP B 501
03AC3SOFTWAREHIS C:34 , HIS C:37 , LEU C:40 , PHE C:148 , GLY C:149 , LYS C:151 , ASP C:152 , PRO C:176 , THR C:177 , VAL C:178 , LEU C:186 , HOH C:290 , HOH C:520 , GOL C:602 , HOH C:603 , HOH C:604 , HOH C:652 , HOH C:675BINDING SITE FOR RESIDUE AMP C 501
04AC4SOFTWAREPRO D:28 , MET D:30 , HIS D:37 , LEU D:40 , PHE D:148 , GLY D:149 , THR D:177 , HOH D:300 , GOL D:604BINDING SITE FOR RESIDUE AMP D 501
05AC5SOFTWAREMET A:30 , GLN A:61 , VAL A:130 , ILE A:133 , GLN A:155 , HOH A:306 , AMP A:501BINDING SITE FOR RESIDUE GOL A 601
06AC6SOFTWAREGLN C:61 , ILE C:133 , GLN C:155 , HOH C:294 , AMP C:501BINDING SITE FOR RESIDUE GOL C 602
07AC7SOFTWAREMET B:30 , GLN B:61 , ILE B:133 , GLN B:155 , HOH B:294 , AMP B:501BINDING SITE FOR RESIDUE GOL B 603
08AC8SOFTWARETHR D:29 , GLN D:61 , VAL D:130 , GLN D:155 , AMP D:501 , HOH D:653BINDING SITE FOR RESIDUE GOL D 604
09AC9SOFTWAREGLN B:260 , HOH B:343 , HOH B:664BINDING SITE FOR RESIDUE GOL B 605
10BC1SOFTWARETYR A:153 , GLN A:260 , HOH A:616BINDING SITE FOR RESIDUE IMD A 606
11BC2SOFTWAREGLN A:61 , ARG A:123 , HIS A:126 , ARG A:189 , HOH A:673BINDING SITE FOR RESIDUE CL A 607

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q10)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q10)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q10)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q10)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q10)

(-) 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 d3q10a_ 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
                 3q10 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: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 d3q10b_ B: 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...hhhhhhhhhhhhhhhh..ee...eeee............eeeeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q10 B   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 C 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 d3q10c_ C: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh...eeeeee..hhhhh..hhhhhh...hhhhhhhhhhhh...eee..hhhhhh........eee.......hhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.ee...eeee............eeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q10 C  -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 D from PDB  Type:PROTEIN  Length:198
 aligned with PANC_YERPE | Q8ZBK7 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:279
                             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         
           PANC_YERPE     - -MLIIETLPLLRQQIRRWRQEGKRIALVPTMGNLHEGHMTLVDEAKTRADVVVVTIFVNPLQFERPDDLAHYPRTLQEDCEKLTRHGADLVFAPAAADIYPAGLEKQTYVDVPALSTILEGASRPGHFRGVSTIVSKLFNLIQPDVACFGEKDYQQLALIRKMVADMGYDINIVGVPTVRAKDGLALSSRNGYLTEEERQIAPQLSKIMWALAEKMALGERQIDALLEEAAAQLLRVGFTPDELFIRDAETLQPLTVDSQQAVILMAAWLGKARLIDNQ 278
               SCOP domains d3q10d_ D: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Pantoate_ligase-3q10D01 D:1-278                                                                                                                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) -Pantoate_ligase-3q10D02 D:1-278                                                                                                                                                                                                                                                        Pfam domains (2)
           Pfam domains (3) -Pantoate_ligase-3q10D03 D:1-278                                                                                                                                                                                                                                                        Pfam domains (3)
           Pfam domains (4) -Pantoate_ligase-3q10D04 D:1-278                                                                                                                                                                                                                                                        Pfam domains (4)
         Sec.struct. author ..eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh...eeeeee..hhhhh.hhhhhhhh..hhhhhhhhhhhh...eee..hhhhhh........eee.......hhhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee..--------------------------------------------------------------.......---------------..eee.----...eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q10 D   0 AMLIIETLPLLRQQIRRWRQEGKRIALVPTMGNLHEGHMTLVDEAKTRADVVVVTIFVNPLQFERPDDLAHYPRTLQEDCEKLTRHGADLVFAPAAADIYPAGLEKQTYVDVPALSTILEGASRPGHFRGVSTIVSKLFNLIQPDVACFGEKDYQQLALIRKMVADMGYDINIVGVPT--------------------------------------------------------------PDELFIR---------------VILMAA----ARLIDNQ 278
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       | -         -         -         -         -         -         -|     |  -         -  |    | -  |      
                                                                                                                                                                                                           177                                                            240   246             262  267  272
   Legend:   → Mismatch (orange background)
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  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 3Q10)

(-) 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

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        PANC_YERPE | Q8ZBK7: 3q12

(-) Related Entries Specified in the PDB File

3q12