3N1T - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE H101A MUTANT ECHINT GMP COMPLEX

Authors :   V. Cody

Date :   17 May 10 (Deposition) - 20 Oct 10 (Release) - 08 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.72

Chains :   Asym. Unit : A,B,E,F
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: E,F  (1x)

Keywords :   Histidine Triad Nucleotide Binding Protein, Hint, Gmp, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Bardaweel, J. Pace, T. F. Chou, V. Cody, C. R. Wagner
Probing The Impact Of The Echint C-Terminal Domain On Structure And Catalysis.
J. Mol. Biol. V. 404 627 2010
PubMed-ID: 20934431 | Reference-DOI: 10.1016/J.JMB.2010.09.066

Molecule 1 - HIT-LIKE PROTEIN HINT
	Chains	:	A, B, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PB429
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	BB2

		1	2	3	4
Asymmetric Unit	:	A	B	E	F
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	5GP	4	Ligand/Ion	GUANOSINE-5'-MONOPHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	5GP	2	Ligand/Ion	GUANOSINE-5'-MONOPHOSPHATE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	5GP	2	Ligand/Ion	GUANOSINE-5'-MONOPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:6 , ILE A:10 , ARG A:30 , ASP A:31 , ILE A:32 , SER A:33 , LEU A:41 , ASN A:88 , GLN A:95 , GLU A:96 , VAL A:97 , HIS A:103 , HOH A:127 , HOH A:132 , HOH A:179 , HOH A:184	BINDING SITE FOR RESIDUE 5GP A 200
2	AC2	SOFTWARE	ARG A:13 , HOH A:183 , ILE B:6 , PHE B:29 , ARG B:30 , ASP B:31 , ILE B:32 , LEU B:41 , ASN B:88 , GLN B:95 , GLU B:96 , VAL B:97 , HIS B:103 , HOH B:121 , HOH B:125 , HOH B:134 , HOH B:141	BINDING SITE FOR RESIDUE 5GP B 200
3	AC3	SOFTWARE	ILE E:6 , ARG E:30 , ASP E:31 , ILE E:32 , SER E:33 , LEU E:41 , ASN E:88 , GLN E:95 , GLU E:96 , VAL E:97 , HIS E:103 , HOH E:121 , HOH E:140 , HOH E:145 , HOH E:147 , HOH E:164 , ARG F:13 , HOH F:185	BINDING SITE FOR RESIDUE 5GP E 200
4	AC4	SOFTWARE	ILE F:6 , PHE F:7 , ILE F:10 , ARG F:30 , ASP F:31 , ILE F:32 , LEU F:41 , ASN F:88 , GLN F:95 , GLU F:96 , VAL F:97 , HIS F:103 , HOH F:123 , HOH F:129 , HOH F:133 , HOH F:156 , HOH F:161 , HOH F:164	BINDING SITE FOR RESIDUE 5GP F 200

(no "SS Bond" information available for 3N1T)

Asymmetric Unit

No.	Residues
1	Gly A:111	-	Pro A:112

(no "SAP(SNP)/Variant" information available for 3N1T)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIT_2	PS51084	HIT domain profile.	HINT_ECOLI	6-115	4	A:6-115 B:6-115 E:6-115 F:6-115
2	HIT_1	PS00892	HIT domain signature.	HINT_ECOLI	88-106	4	A:88-106 B:88-106 E:88-106 F:88-106

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIT_2	PS51084	HIT domain profile.	HINT_ECOLI	6-115	2	A:6-115 B:6-115 - -
2	HIT_1	PS00892	HIT domain signature.	HINT_ECOLI	88-106	2	A:88-106 B:88-106 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIT_2	PS51084	HIT domain profile.	HINT_ECOLI	6-115	2	- - E:6-115 F:6-115
2	HIT_1	PS00892	HIT domain signature.	HINT_ECOLI	88-106	2	- - E:88-106 F:88-106

(no "Exon" information available for 3N1T)

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:114
 aligned with HINT_ECOLI | P0ACE7 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:114
                                    12        22        32        42        52        62        72        82        92       102       112    
           HINT_ECOLI     3 EETIFSKIIRREIPSDIVYQDDLVTAFRDISPQAPTHILIIPNILIPTVNDVSAEHEQALGRMITVAAKIAEQEGIAEDGYRLIMNTNRHGGQEVYHIHMHLLGGRPLGPMLAH 116
               SCOP domains d3n1ta_ A: automated matches                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhh......eeee...eeeee.......eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeehhhhh.......eeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---HIT_2  PDB: A:6-115 UniProt: 6-115                                                                            - PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------HIT_1  PDB: A:88-10---------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3n1t A   3 EETIFSKIIRREIPSDIVYQDDLVTAFRDISPQAPTHILIIPNILIPTVNDVSAEHEQALGRMITVAAKIAEQEGIAEDGYRLIMNTNRHGGQEVYHIAMHLLGGRPLGPMLAH 116
                                    12        22        32        42        52        62        72        82        92       102       112

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with HINT_ECOLI | P0ACE7 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           HINT_ECOLI     2 AEETIFSKIIRREIPSDIVYQDDLVTAFRDISPQAPTHILIIPNILIPTVNDVSAEHEQALGRMITVAAKIAEQEGIAEDGYRLIMNTNRHGGQEVYHIHMHLLGGRPLGPMLAHKG 118
               SCOP domains d3n1tb_ B: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh........ee...eeeee.......eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeehhhhh.......eeeee............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----HIT_2  PDB: B:6-115 UniProt: 6-115                                                                            --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------HIT_1  PDB: B:88-10------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3n1t B   2 AEETIFSKIIRREIPSDIVYQDDLVTAFRDISPQAPTHILIIPNILIPTVNDVSAEHEQALGRMITVAAKIAEQEGIAEDGYRLIMNTNRHGGQEVYHIAMHLLGGRPLGPMLAHKG 118
                                    11        21        31        41        51        61        71        81        91       101       111

Chain E from PDB  Type:PROTEIN  Length:112
 aligned with HINT_ECOLI | P0ACE7 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:112
                                    13        23        33        43        53        63        73        83        93       103       113  
           HINT_ECOLI     4 ETIFSKIIRREIPSDIVYQDDLVTAFRDISPQAPTHILIIPNILIPTVNDVSAEHEQALGRMITVAAKIAEQEGIAEDGYRLIMNTNRHGGQEVYHIHMHLLGGRPLGPMLA 115
               SCOP domains d3n1te_ E: automated matches                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh......eeee...eeeee.......eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeehhhhh.......eeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --HIT_2  PDB: E:6-115 UniProt: 6-115                                                                             PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------HIT_1  PDB: E:88-10--------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 3n1t E   4 ETIFSKIIRREIPSDIVYQDDLVTAFRDISPQAPTHILIIPNILIPTVNDVSAEHEQALGRMITVAAKIAEQEGIAEDGYRLIMNTNRHGGQEVYHIAMHLLGGRPLGPMLA 115
                                    13        23        33        43        53        63        73        83        93       103       113

Chain F from PDB  Type:PROTEIN  Length:115
 aligned with HINT_ECOLI | P0ACE7 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:115
                                    12        22        32        42        52        62        72        82        92       102       112     
           HINT_ECOLI     3 EETIFSKIIRREIPSDIVYQDDLVTAFRDISPQAPTHILIIPNILIPTVNDVSAEHEQALGRMITVAAKIAEQEGIAEDGYRLIMNTNRHGGQEVYHIHMHLLGGRPLGPMLAHK 117
               SCOP domains d3n1tf_ F: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------HIT-3n1tF01 F:12-110                                                                               ------- Pfam domains (1)
           Pfam domains (2) ---------HIT-3n1tF02 F:12-110                                                                               ------- Pfam domains (2)
           Pfam domains (3) ---------HIT-3n1tF03 F:12-110                                                                               ------- Pfam domains (3)
           Pfam domains (4) ---------HIT-3n1tF04 F:12-110                                                                               ------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhh......eeee...eeeee.......eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeehhhhh.......eeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---HIT_2  PDB: F:6-115 UniProt: 6-115                                                                            -- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------HIT_1  PDB: F:88-10----------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3n1t F   3 EETIFSKIIRREIPSDIVYQDDLVTAFRDISPQAPTHILIIPNILIPTVNDVSAEHEQALGRMITVAAKIAEQEGIAEDGYRLIMNTNRHGGQEVYHIAMHLLGGRPLGPMLAHK 117
                                    12        22        32        42        52        62        72        82        92       102       112

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: HIT-like (73)

Superfamily: HIT-like (67)

Family: automated matches (11)

Protein domain: automated matches (11)

Escherichia coli [TaxId: 562] (2)

1a	d3n1ta_	A:
1b	d3n1te_	E:
1c	d3n1tf_	F:
1d	d3n1tb_	B:

(no "CATH Domain" information available for 3N1T)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HIT (23)

Family: HIT (19)

Escherichia coli (strain K12) (2)

1a	HIT-3n1tF01	F:12-110
1b	HIT-3n1tF02	F:12-110
1c	HIT-3n1tF03	F:12-110
1d	HIT-3n1tF04	F:12-110

Asymmetric Unit(hide GO term definitions)

Chain A,B,E,F (HINT_ECOLI | P0ACE7)

molecular function
	GO:0043530	adenosine 5'-monophosphoramidase activity	Catalysis of the reaction: adenosine 5'-monophosphoramidate = AMP + NH2. Other substrates include AMP-morpholidate, AMP-N-alanine methyl ester and AMP-alpha-acetyl lysine methyl ester.
	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:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	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.
biological process
	GO:0055130	D-alanine catabolic process	The chemical reactions and pathways resulting in the breakdown of D-alanine, the D-enantiomer of the amino acid alanine.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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		Gly A:111 - Pro A:112	[ RasMol ]

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	3n1t
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	HINT_ECOLI \| P0ACE7	:	3n1s

1av5	HUMAN HINT
3n1s	NATIVE ECHINT WITH GMP BOUND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

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