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(-) Description

Title :  THE STRUCTURE OF HISTIDINE INHIBITED HISG FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
 
Authors :  B. Lohkamp, T. Schweikert, A. J. Lapthorn
Date :  28 Sep 07  (Deposition) - 04 Nov 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Metal-Binding, Glycosyltransferase, Hisg, Histidine, Magnesium, Transferase, Histidine Biosynthesis, Amino-Acid Biosynthesis, Atp Phosphoribosyl Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Lohkamp, T. Schweikert, A. J. Lapthorn
The Structure Of Histidine Inhibited Hisg From Methanobacterium Thermoautotrophicum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ATP PHOSPHORIBOSYLTRANSFERASE
    Atcc: 29183
    Chains: A, B
    EC Number: 2.4.2.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: RESIDUES 2-287
    Organism Scientific: METHANOBACTERIUM THERMOAUTOTROPHICUM
    Organism Taxid: 187420
    Strain: DELTAH
    Synonym: ATP-PRTASE, ATP-PRT

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 29)

Asymmetric Unit (6, 29)
No.NameCountTypeFull Name
1CL9Ligand/IonCHLORIDE ION
2HIS2Mod. Amino AcidHISTIDINE
3IMD3Ligand/IonIMIDAZOLE
4MG9Ligand/IonMAGNESIUM ION
5MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 1 (4, 33)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HIS6Mod. Amino AcidHISTIDINE
3IMD9Ligand/IonIMIDAZOLE
4MG-1Ligand/IonMAGNESIUM ION
5MPD15Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6MRD3Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:160BINDING SITE FOR RESIDUE CL A1007
02AC2SOFTWAREGLU A:125 , ASP A:134 , ALA A:135BINDING SITE FOR RESIDUE IMD A1288
03AC3SOFTWARELYS A:260 , HOH A:2009BINDING SITE FOR RESIDUE IMD A1289
04AC4SOFTWAREMET A:218 , LEU A:219 , ASN A:220 , GLY A:235 , MET A:236 , THR A:237 , GLY A:238 , THR A:240 , VAL A:256 , ASP A:276BINDING SITE FOR RESIDUE HIS A1290
05AC5SOFTWAREPRO A:1 , LYS A:194 , GLY A:196 , ILE A:197BINDING SITE FOR RESIDUE CL A1291
06AC6SOFTWARELYS A:183BINDING SITE FOR RESIDUE CL A1292
07AC7SOFTWAREGLU A:119 , THR A:157BINDING SITE FOR RESIDUE CL A1293
08AC8SOFTWAREASP A:158 , LEU A:159BINDING SITE FOR RESIDUE MG A1294
09AC9SOFTWAREGLU A:82BINDING SITE FOR RESIDUE MG A1295
10BC1SOFTWAREGLU A:22 , GLY A:27 , GLN A:41BINDING SITE FOR RESIDUE MG A1296
11BC2SOFTWAREASP A:175BINDING SITE FOR RESIDUE MG A1297
12BC3SOFTWAREGLU A:119 , GLU A:139 , LEU A:140 , THR A:141BINDING SITE FOR RESIDUE MPD A1298
13BC4SOFTWAREGLY A:151 , VAL A:152 , ASP A:154BINDING SITE FOR RESIDUE MRD A1299
14BC5SOFTWAREARG A:4 , GLU A:46 , ALA A:63 , ASP A:65 , LYS A:194BINDING SITE FOR RESIDUE MPD A1300
15BC6SOFTWAREASP A:61 , GLU B:136BINDING SITE FOR RESIDUE MG B1118
16BC7SOFTWARELYS B:88 , ASP B:109 , ASP B:258BINDING SITE FOR RESIDUE IMD B1288
17BC8SOFTWAREGLU B:119 , THR B:157BINDING SITE FOR RESIDUE CL B1289
18BC9SOFTWAREPRO B:1 , GLY B:196 , ILE B:197BINDING SITE FOR RESIDUE CL B1290
19CC1SOFTWARELEU B:171 , ARG B:172 , VAL B:173BINDING SITE FOR RESIDUE CL B1291
20CC2SOFTWAREALA B:52 , ALA B:53BINDING SITE FOR RESIDUE CL B1292
21CC3SOFTWARELYS B:10 , ARG B:51 , ALA B:52BINDING SITE FOR RESIDUE MG B1293
22CC4SOFTWAREGLU B:145 , ASP B:158BINDING SITE FOR RESIDUE MG B1294
23CC5SOFTWAREGLY B:11 , ARG B:12 , SER B:14 , GLU B:15BINDING SITE FOR RESIDUE MG B1295
24CC6SOFTWARESER B:9 , HOH B:2001 , HOH B:2006BINDING SITE FOR RESIDUE MG B1296
25CC7SOFTWAREGLU B:119 , GLU B:139 , LEU B:140 , THR B:141BINDING SITE FOR RESIDUE MPD B1297
26CC8SOFTWARELYS B:2 , ARG B:4 , ALA B:63 , ASP B:65BINDING SITE FOR RESIDUE MPD B1298
27CC9SOFTWARESER B:93 , SER B:160 , SER B:161 , GLY B:163BINDING SITE FOR RESIDUE MPD B1299
28DC1SOFTWARELEU B:219 , ASN B:220 , GLY B:235 , MET B:236 , THR B:237 , GLY B:238 , THR B:240 , ALA B:255 , VAL B:256 , ASP B:276 , HOH B:2022BINDING SITE FOR RESIDUE HIS B1300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VD3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VD3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VD3)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATP_P_PHORIBOSYLTRPS01316 ATP phosphoribosyltransferase signature.HIS1_METTH145-166
 		  2A:145-166
B:145-166
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ATP_P_PHORIBOSYLTRPS01316 ATP phosphoribosyltransferase signature.HIS1_METTH145-166
 		  6A:145-166
B:145-166

(-) Exons   (0, 0)

(no "Exon" information available for 2VD3)

(-) 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:290
 aligned with HIS1_METTH | O27550 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:290
                              1                                                                                                                                                                                                                                                                                           287 
                              |      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        |-
          HIS1_METTH      - --MKIRIAVPSKGRISEPAIRLLENAGVGLKDTVNRKLFSKTQHPQIEVMFSRAADIPEFVADGAADLGITGYDLIVERGSDVEILEDLKYGRASLVLAAPEDSTIRGPEDIPRGAVIATEFPGITENYLREHGIDAEVVELTGSTEIAPFIGVADLITDLSSTGTTLRMNHLRVIDTILESSVKLIANRESYATKSGIIEELRTGIRGVIDAEGKRLVMLNIDRKNLDRVRALMPGMTGPTVSEVLSDNGVVAVHAVVDEKEVFNLINRLKAVGARDILVVPIERIIP-    -
               SCOP domains d2vd3a1 A:-1-212 automated matches                                                                                                                                                                                    d2vd3a2 A:213-287 automated matches                                        - SCOP domains
               CATH domains -------------------------------------------------------------------------------------------2vd3A02 A:90-180 Periplasmic binding protein-like II                                       ---------------------------------2vd3A03 A:214-287  [code=3.30.70.120, no name defined]                    - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhh...ee.......eeee....eeeeee...hhhhhhhh....eeeeehhhhhhhh...eeeee.....eeeeeeee......hhhhh....eeee.hhhhhhhhhhhh....eeee...hhhhh.......eeeeee..hhhhhhh.eeeeeeeeee.eeeeehhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhh......eeee......eeeeeeeee..hhhhhhhhhhh...eeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------ATP_P_PHORIBOSYLTR    -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2vd3 A   -1 AVPKIRIAVPSKGRISEPAIRLLENAGVGLKDTVNRKLFSKTQHPQIEVMFSRAADIPEFVADGAADLGITGYDLIVERGSDVEILEDLKYGRASLVLAAPEDSTIRGPEDIPRGAVIATEFPGITENYLREHGIDAEVVELTGSTEIAPFIGVADLITDLSSTGTTLRMNHLRVIDTILESSVKLIANRESYATKSGIIEELRTGIRGVIDAEGKRLVMLNIDRKNLDRVRALMPGMTGPTVSEVLSDNGVVAVHAVVDEKEVFNLINRLKAVGARDILVVPIERIIPH 1290
                                     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      1290
                                                                                                                                                                                                                                                                                                                          287|
                                                                                                                                                                                                                                                                                                                          1290


Chain B from PDB  Type:PROTEIN  Length:289
 aligned with HIS1_METTH | O27550 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:290
                              1                                                                                                                                                                                                                                                                                           287 
                              |      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        |-
          HIS1_METTH      - --MKIRIAVPSKGRISEPAIRLLENAGVGLKDTVNRKLFSKTQHPQIEVMFSRAADIPEFVADGAADLGITGYDLIVERGSDVEILEDLKYGRASLVLAAPEDSTIRGPEDIPRGAVIATEFPGITENYLREHGIDAEVVELTGSTEIAPFIGVADLITDLSSTGTTLRMNHLRVIDTILESSVKLIANRESYATKSGIIEELRTGIRGVIDAEGKRLVMLNIDRKNLDRVRALMPGMTGPTVSEVLSDNGVVAVHAVVDEKEVFNLINRLKAVGARDILVVPIERIIP-    -
               SCOP domains d2vd3b1 B:-1-212 automated matches                                                                                                                                                                                    d2vd3b2 B:213-287 automated matches                                        - SCOP domains
               CATH domains -------------------------------------------------------------------------------------------2vd3B02 B:90-180 Periplasmic binding protein-like II                                       ---------------------------------2vd3B03 B:214-287  [code=3.30.70.120, no name defined]                    - CATH domains
           Pfam domains (1) ---------------------------------------------------HisG-2vd3B03 B:50-209                                                                                                                                           HisG_C-2vd3B01 B:210-285                                                    --- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------HisG-2vd3B04 B:50-209                                                                                                                                           HisG_C-2vd3B02 B:210-285                                                    --- Pfam domains (2)
         Sec.struct. author ....eeeeee....hhhhhhhhhhhh...ee...-...eeee....eeeeee...hhhhhhhh....eeeeehhhhhhhh...eeeee.....eeeeeeee......hhhhh....eeee.hhhhhhhhhhhhh...eeee...hhhhhhhhh...eeeeee..hhhhhhh.eeeeeeeeee.eeeeehhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..hhhhhhhhh......eeee......eeeeeeeeehhhhhhhhhhhhhh..eeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------ATP_P_PHORIBOSYLTR    -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2vd3 B   -1 AVPKIRIAVPSKGRISEPAIRLLENAGVGLKDTV-RKLFSKTQHPQIEVMFSRAADIPEFVADGAADLGITGYDLIVERGSDVEILEDLKYGRASLVLAAPEDSTIRGPEDIPRGAVIATEFPGITENYLREHGIDAEVVELTGSTEIAPFIGVADLITDLSSTGTTLRMNHLRVIDTILESSVKLIANRESYATKSGIIEELRTGIRGVIDAEGKRLVMLNIDRKNLDRVRALMPGMTGPTVSEVLSDNGVVAVHAVVDEKEVFNLINRLKAVGARDILVVPIERIIPH 1300
                                     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      1300
                                                            32 |                                                                                                                                                                                                                                                          287|
                                                              34                                                                                                                                                                                                                                                          1300
   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  (2, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: GlnB-like (50)
(-)
Clan: PBP (391)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HIS1_METTH | O27550)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003879    ATP phosphoribosyltransferase activity    Catalysis of the reaction: 1-(5-phospho-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0000105    histidine biosynthetic process    The chemical reactions and pathways resulting in the formation of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid.
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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