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(-) Description

Title :  CRYSTAL STRUCTURE OF PANTOATE--BETA-ALANINE LIGASE (PANC) FROM THERMOTOGA MARITIMA
 
Authors :  B. Bagautdinov, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  16 Mar 07  (Deposition) - 18 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Pantoate-Beta-Alanine Ligase, X-Ray Diffraction, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bagautdinov, N. Kunishima
Crystal Structure Of Pantoate--Beta-Alanine Ligase (Panc) From Thermotoga Maritima
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PANTOATE--BETA-ALANINE LIGASE
    Chains: A
    EC Number: 6.3.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: (DE3)RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PANC
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: PANTOTHENATE SYNTHETASE, PANTOATE-ACTIVATING ENZYME

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 23)

Asymmetric Unit (2, 23)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ZN22Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:8 , GLU A:97 , HOH A:1242BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWAREMET A:1 , GLU A:16 , GLU A:19BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWAREHIS A:92 , HOH A:1229BINDING SITE FOR RESIDUE ZN A 503
04AC4SOFTWAREHIS A:115 , HOH A:1211 , HOH A:1247 , HOH A:1248BINDING SITE FOR RESIDUE ZN A 504
05AC5SOFTWAREHIS A:142 , GLU A:169 , HOH A:1141BINDING SITE FOR RESIDUE ZN A 505
06AC6SOFTWAREGLU A:194 , GLU A:221 , GLU A:254BINDING SITE FOR RESIDUE ZN A 506
07AC7SOFTWAREASP A:219 , ASP A:235 , HOH A:1257BINDING SITE FOR RESIDUE ZN A 507
08AC8SOFTWAREHIS A:230 , GLU A:251 , HOH A:1262BINDING SITE FOR RESIDUE ZN A 508
09AC9SOFTWARECYS A:117 , ASP A:240 , HOH A:1266BINDING SITE FOR RESIDUE ZN A 509
10BC2SOFTWAREHIS A:37 , LYS A:149 , SER A:186BINDING SITE FOR RESIDUE ZN A 511
11BC3SOFTWAREHIS A:37 , HOH A:1198BINDING SITE FOR RESIDUE ZN A 512
12BC4SOFTWAREGLN A:61 , GLY A:63 , GLU A:66 , HIS A:124 , HOH A:1120BINDING SITE FOR RESIDUE ZN A 513
13BC5SOFTWAREGLU A:210BINDING SITE FOR RESIDUE ZN A 515
14BC6SOFTWARELYS A:207 , GLU A:210BINDING SITE FOR RESIDUE ZN A 516
15BC7SOFTWARECYS A:117 , HOH A:1274 , HOH A:1278BINDING SITE FOR RESIDUE ZN A 517
16BC8SOFTWARECYS A:117BINDING SITE FOR RESIDUE ZN A 518
17BC9SOFTWAREGLU A:5 , HOH A:1223 , HOH A:1241BINDING SITE FOR RESIDUE ZN A 519
18CC1SOFTWAREILE A:208 , HIS A:230 , GLU A:251 , HOH A:1256BINDING SITE FOR RESIDUE ZN A 521
19CC2SOFTWAREGLU A:19BINDING SITE FOR RESIDUE ZN A 522
20CC3SOFTWAREGLU A:96 , LYS A:222BINDING SITE FOR RESIDUE ACT A 1101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EJC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EJC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EJC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EJC)

(-) Exons   (0, 0)

(no "Exon" information available for 2EJC)

(-) 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:280
 aligned with PANC_THEMA | Q9X0G6 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:280
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280
           PANC_THEMA     1 MRIIETIEEMKKFSEEMREKKKTIGFVPTMGYLHEGHLSLVRRARAENDVVVVSIFVNPTQFGPNEDYERYPRDFERDRKLLEKENVDCIFHPSVEEMYPPDFSTYVEETKLSKHLCGRSRPGHFRGVCTVVTKLFNIVKPHRAYFGQKDAQQFRVLRRMVRDLNMDVEMIECPIVREPDGLAMSSRNVYLSPEERQQALSLYQSLKIAENLYLNGERDAEKIKEEMIKHLSRFDKVKIDYVEIVDEETLEPVEKIDRKVIVAVAAWVGNARLIDNTILG 280
               SCOP domains d2ejca_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                  SCOP domains
               CATH domains -2ejcA01 A:2-177 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                           2ejcA02 A:178-277  [code=3.30.1300.10, no name defined]                                             --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhh.eeeeee..hhhhh....hhhhh..hhhhhhhhhhh....eee..hhhhhh...........hhhhh.hhhhh.hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...eeeeeeeeee.............eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ejc A   1 MRIIETIEEMKKFSEEMREKKKTIGFVPTMGYLHEGHLSLVRRARAENDVVVVSIFVNPTQFGPNEDYERYPRDFERDRKLLEKENVDCIFHPSVEEMYPPDFSTYVEETKLSKHLCGRSRPGHFRGVCTVVTKLFNIVKPHRAYFGQKDAQQFRVLRRMVRDLNMDVEMIECPIVREPDGLAMSSRNVYLSPEERQQALSLYQSLKIAENLYLNGERDAEKIKEEMIKHLSRFDKVKIDYVEIVDEETLEPVEKIDRKVIVAVAAWVGNARLIDNTILG 280
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EJC)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (PANC_THEMA | Q9X0G6)
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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